Pyrimido-diazepinone kinase scaffold compounds and methods of treating dclk1/2-mediated disorders

ABSTRACT

The present invention relates to use of pyrimido-diazepinone compounds that are able to modulate protein kinases such as doublecortin-like kinase (DCLK1) and doublecortin-like kinase 2 (DCLK2), which are members of serine/threonine-protein kinase family and Ca2+/calmodulin-dependent protein kinase class of enzymes, and the use of such compounds in the treatment of various diseases, disorders or conditions.

RELATED APPLICATIONS

This application claims the benefit of priority under 35 U.S.C. § 119(e)to U.S. Provisional Application No. 62/409,457, filed Oct. 18, 2016,which is incorporated herein by reference in its entirety.

TECHNICAL FIELD

The present invention relates to pyrimido-diazepinone compounds whichare able to modulate protein kinases such as doublecortin-like kinase 1(DCLK1) and doublecortin-like kinase 2 (DCLK2), which are members ofserine/threonine-protein kinase family and Ca²⁺/calmodulin-dependentprotein kinase class of enzymes, and the use of such compounds in thetreatment of various diseases, disorders or conditions.

BACKGROUND OF THE INVENTION

Protein kinases represent a large family of proteins, which play acentral role in the regulation of a wide variety of cellular processesand maintaining control over cellular function. Protein kinasesconstitute a large family of structurally related enzymes that areresponsible for the control of a variety of signal transductionprocesses within the cell (see Hardie, G and Hanks, S. The ProteinKinase Facts Book, I and II, Academic Press, San Diego, Calif.: 1995).Protein kinases are thought to have evolved from a common ancestral genedue to the conservation of their structure and catalytic function.Almost all kinases contain a similar 250-300 amino acid catalyticdomain. The kinases may be categorized into families by the substratesthey phosphorylate (e.g., protein-tyrosine, protein-serine/threonine,lipids etc).

In general, protein kinases mediate intracellular signaling bycatalyzing a phosphoryl transfer from a nucleoside triphosphate to aprotein acceptor that is involved in a signaling pathway. Thesephosphorylation events act as molecular on/off switches that canmodulate or regulate the target protein biological function. Thesephosphorylation events are ultimately triggered in response to a varietyof extracellular and other stimuli. Examples of such stimuli includeenvironmental and chemical stress signals (e.g., shock, heat shock,ultraviolet radiation, bacterial endotoxin, and H2O2), cytokines (e.g.,interleukin-1 (IL-I) and tumor necrosis factor alpha (TNF-a), and growthfactors (e.g., granulocyte macrophage-colony stimulating factor(GM-CSF), and fibroblast growth factor (FGF)). An extracellular stimulusmay affect one or more cellular responses related to cell growth,migration, differentiation, secretion of hormones, activation oftranscription factors, muscle contraction, glucose metabolism, controlof protein synthesis, survival and regulation of the cell cycle.

Described herein are compounds that inhibit the activity of one or moreisoforms of the protein kinase DCLK1/2 and are, therefore, expected tobe useful in the treatment of kinase-associated diseases.

SUMMARY OF THE INVENTION

In one aspect, the invention provides a method of treating a diseasemediated by a kinase such as doublecortin-like kinase 1 (DCLK1) and/ordoublecortin-like kinase 2 (DCLK2). The method comprises administeringof a kinase inhibitor compound, e.g., a compound of formula A:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

X is CHR₄, CR₄, NH, NR₄ or N;

Y is NR₅, N, S, SO, SO₂, O, CHR₅, or CR₅; wherein at least one of X andY is NH, NR₄, NR₅, N, S, SO, SO₂, or O;

A is a single bond or double bond;

B is a single bond or double bond, wherein both A and B are not doublebonds;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₄ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

or R₃ and X, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted;

or X and Y, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted; and

R₆ is hydrogen or optionally substituted alkyl.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or DCLK2 comprises administering tothe subject a compound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₅ is hydrogen, optionally substituted alkyl, optionally substitutedaralkyl, or optionally substituted carbocyclic; and

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In some embodiments, R₅ is methyl.

In some embodiments, R₂ is unsubstituted alkyl.

In some embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, each ofwhich may be optionally substituted with one or more halogen.

In some embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In some embodiments, the compound is of formula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl, s-butyl,t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino, phenyl,1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl, pyridizinyl,quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl, pyrrolyl, furanyl,isoquinolinyl, imiazolyl, or triazolyl, each of which may be optionallysubstituted.

In embodiments, R₁ is phenyl or pyridyl, each of which may be optionallysubstituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom alkoxy, CO₂Me,

In embodiments, R₁ is phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl,pyrazolyl, imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each ofwhich may be optionally substituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, carbocyclic, SO₂(R_(A)), SO₃ (R_(A)), SO₂N(R_(A)) (R_(A)),SO₂NH(R_(A)), SO₂NH₂, PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each ofwhich may be further substituted; and each R_(A) is independentlyselected from alkyl, alkenyl, carbocyclic, aryl, heteroaryl, andheterocyclic, or two R_(A) on the same atom combine to form aheterocyclic, each of which may be further substituted.

In some embodiments, R₁ is selected from the group consisting of:

In embodiments, the compound inhibits DCLK1 and/or DCLK2.

In embodiments, the disease is cancer or a proliferation disease.

In some embodiments, the disease is lung, colon, breast, prostate,liver, pancreas, brain, kidney, ovaries, stomach, skin, and bonecancers, gastric, breast, pancreatic cancer, glioma, and hepatocellularcarcinoma, papillary renal carcinoma, head and neck squamous cellcarcinoma, leukemias, lymphomas, myelomas, solid tumors, or blood-bornecancers (e.g., chronic lymphocytic leukemia (CLL), follicular lymphoma(FL), or indolent non-Hodgkin's lymphoma (iNHL).

In some embodiments, the disease is Barretts' esophagus, esophagealcancer, salivary gland malignancies, colon and colorectal cancer,intestinal cancer, gastric cancer, pancreatic cancer, skin cancer orneuroblastoma.

In embodiments, the disease is a liver disease.

In some embodiments, the disease is a fatty liver disease, non-alcoholicfatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH),cirrhosis, fatty liver disease resulting from hepatitis, fatty liverdisease resulting from obesity, fatty liver disease resulting fromdiabetes, fatty liver disease resulting from insulin resistance, fattyliver disease resulting from hypertriglyceridemia, Abetalipoproteinemia,glycogen storage diseases, Wolmans disease, or acute fatty liver ofpregnancy.

In embodiments, the disease is a neurodegenerative disease.

In some embodiments, the disease is Alzheimer's disease (AD),Parkinson's disease (PD), Huntington's (HD) diseases, amyotrophiclateral sclerosis (ALS), spinal muscular atrophy (SMA), schizophrenia,attention-deficit/hyperactivity disorder (ADHD), fetal alcohol syndromeand diabetic encephalopathy.

In embodiments, the subject is administered an additional therapeuticagent.

In embodiments, said additional therapeutic agent are administeredsimultaneously or sequentially.

In embodiments, said additional therapeutic agent is a chemotherapeuticagent.

In one aspect, a method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprises contacting a cell with acompound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₅ is hydrogen, optionally substituted alkyl, optionally substitutedaralkyl, or optionally substituted carbocyclic; and

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment comprisesadministering a compound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₅ is hydrogen, optionally substituted alkyl, optionally substitutedaralkyl, or optionally substituted carbocyclic; and

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In embodiments, the subject is a human.

In embodiments, the compound has a Ki for inhibiting thedoublecortin-like kinase (DCLK1/2) less than about 1 μM, less than about500 nM, less than about 100 nM, less than about 50 nM, less than about40 nM, less than about 30 nM, less than about 20 nM, or less than about15 nM.

In some embodiments, R₅ is methyl.

In some embodiments, R₂ is unsubstituted alkyl.

In some embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, each ofwhich may be optionally substituted with one or more halogen.

In some embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In embodiments, the compound is of formula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl, s-butyl,t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino, phenyl,1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl, pyridizinyl,quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl, pyrrolyl, furanyl,isoquinolinyl, imiazolyl, or triazolyl, each of which may be optionallysubstituted.

In embodiments, R₁ is phenyl or pyridyl, each of which may be optionallysubstituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;

wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom alkoxy, CO₂Me,

In embodiments, R₁ is phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl,pyrazolyl, imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each ofwhich may be optionally substituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, carbocyclic, SO₂(R_(A)), SO₃(R_(A)), S₂N(R_(A)) (R_(A)),SO₂NH(R_(A)), SO₂NH₂, PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each ofwhich may be further substituted; and

wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In some embodiments, R₁ is selected from the group consisting of:

In one aspect, the method of treating a disease in a subject mediated bya kinase such as doublecortin-like kinase (DCLK1/2) comprisesadministering to the subject a compound of formula A-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

X is CHR₄, CR₄, NH, NR₄ or N;

Y is NR₅, N, S, SO, SO₂, O, CHR₅, or CR₅; wherein at least one of X andY is NH, NR₄, NR₅, N, S, SO, SO₂, or O;

A is a single bond or double bond;

B is a single bond or double bond, wherein both A and B are not doublebonds;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₄ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

or R₃ and X, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted;

or X and Y, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula A-1, or a pharmaceutically acceptable salt, ester orprodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula A-1, or apharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, the compound has a structure according to formula B-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is aryl, or heteroaryl, wherein R₁ may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen or methyl;

R₄ is hydrogen or methyl; and

R₆ is hydrogen.

In embodiments, the compound has a structure according to formula C-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is aryl, heteroaryl, which may be optionally substituted;

R₂ is hydrogen or methyl;

R₃ is hydrogen;

R₄ is hydrogen; and

R₆ is hydrogen.

In embodiments, the compound has a structure according to formula D-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-6.

In embodiments, the compound has a structure according to formula E-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-6.

In embodiments, the compound has a structure according to formula F-I:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

Y is S, SO, SO₂, N, or O;

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In embodiments, the compound has a structure according to formula G-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3 heteroatomsselected from O, S, or N; or R₁ is aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, wherein R₁ may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted; and

R₆ is hydrogen or optionally substituted alkyl.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2) comprises administering to the subject a compound of formulaI-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

A is a single bond or double bond;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula I-2, or a pharmaceutically acceptable salt, ester orprodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula I-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2) comprises comprising administering to the subject a compound offormula II-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

E is NR₂ or CHR₂;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula II-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula II-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject wherein thedisease is mediated by doublecortin-like kinase (DCLK1) and/ordoublecortin-like kinase 2 (DCLK2), the method comprising administeringto the subject a compound of formula III-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula III-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula III-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject wherein thedisease is mediated by doublecortin-like kinase (DCLK1) and/ordoublecortin-like kinase 2 (DCLK2), the method comprising administeringto the subject a compound of formula IV-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula IV-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula IV-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2), the method comprising administering to the subject a compoundof formula V-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

X is an optional substituent as defined for formula I;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is —OH or —O-(optionally substituted alkyl);

R₄ is hydrogen or optionally substituted alkyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula V-2, or a pharmaceutically acceptable salt, ester orprodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula V-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2), the method comprising administering to the subject a compoundof formula VI-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; or

two X moieties on adjacent atoms of the thiophene ring can form,together with the atoms to which they are attached, a phenyl ring; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula VI-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula VI-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject wherein thedisease is mediated by doublecortin-like kinase (DCLK1) and/ordoublecortin-like kinase 2 (DCLK2), the method comprising administeringto the subject a compound of formula VII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula VII-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula VII-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2), the method comprising administering to the subject a compoundof formula VIII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

Z is O or S;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula VIII-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula VIII-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the method of treating a disease in a subject mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2), the method comprising administering to the subject a compoundof formula IX-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

A is a single bond or double bond;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

Y is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ and R₂′ are each independently hydrogen, optionally substitutedalkyl, optionally substituted cycloalkyl, and optionally substitutedheterocyclyl;

or Y and R₂′ can form, together with the atoms to which they areattached, a five-membered ring; and

R₆ is hydrogen or optionally substituted alkyl.

In another aspect, the method for reducing doublecortin-like kinase(DCLK1/2)-dependent cell growth comprising contacting a cell with acompound of formula IX-2, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In another aspect, the method of inhibiting doublecortin-like kinase(DCLK1/2) in a subject identified as in need of such treatment,comprising administering a compound of formula IX-2, or apharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the present invention provides a compound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₅ is hydrogen, optionally substituted alkyl, optionally substitutedaralkyl, or optionally substituted carbocyclic; and

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In embodiments, R₅ is methyl.

In embodiments, R₂ is unsubstituted alkyl.

In some embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, each ofwhich may be optionally substituted with one or more halogen.

In some embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In embodiments, the compound is of formula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, R₂ is unsubstituted alkyl.

In some embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, each ofwhich may be optionally substituted with one or more halogen.

In some embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl, s-butyl,t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino, phenyl,1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl, pyridizinyl,quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl, pyrrolyl, furanyl,isoquinolinyl, imiazolyl, or triazolyl, each of which may be optionallysubstituted.

In some embodiments, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;

wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom alkoxy, CO₂Me,

In embodiments, R₁ is phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl,pyrazolyl, imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each ofwhich may be optionally substituted.

In some embodiments, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, carbocyclic, SO₂(R_(A)), SO₃ (R_(A)), SO₂N(R_(A)) (R_(A)),SO₂NH(R_(A)), SO₂NH₂, PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each ofwhich may be further substituted; and

wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In some embodiments, R₁ is selected from the group consisting of:

In embodiments, the compound of formula F-1-a inhibits DCLK1 and/orDCLK2.

Further provided in the present invention is a pharmaceuticalcomposition comprising the compound (e.g. formula F-1, formula F-1-a,formula A-1 and etc.) as described herein, or a pharmaceuticallyacceptable salt, ester or prodrug thereof.

Additionally, in one aspect, the intention provides methods of treatinga disease in a subject, wherein the disease is mediated bydoublecortin-like kinase (DCLK1) and/or doublecortin-like kinase 2(DCLK2), the method comprising administering to the subject the compoundas described herein, or a pharmaceutically acceptable salt, ester orprodrug thereof.

In another aspect, the invention provides methods for reducingdoublecortin-like kinase (DCLK1/2)-dependent cell growth comprisingcontacting a cell with the compound as described herein, or apharmaceutically acceptable salt, ester or prodrug thereof.

In another aspect, the invention provides methods of inhibitingdoublecortin-like kinase (DCLK1/2) in a subject identified as in need ofsuch treatment, comprising administering the compound as describedherein, or a pharmaceutically acceptable salt, ester or prodrug thereof.

In one aspect, the invention features a method of treating a disease ina subject mediated by a kinase that is doublecortin-like kinase(DCLK1/2) comprising administering to the subject a compound asdescribed herein (e.g., a compound of formula F-1, formula F-1-a orformula A-1), or a pharmaceutically acceptable salt, ester or prodrugthereof.

In another aspect, the invention features a method for reducingdoublecortin-like kinase (DCLK1/2)-dependent cell growth comprisingcontacting a cell with a compound as described herein (e.g., a compoundof formula F-1, formula F-1-a or formula A-1) or a pharmaceuticallyacceptable salt, ester or prodrug thereof.

In another aspect, the invention features a method of inhibitingdoublecortin-like kinase (DCLK1/2) in a subject identified as in need ofsuch treatment, comprising administering a compound as described (e.g.,a compound of formula F-1, formula F-1-a or formula A-1), or apharmaceutically acceptable salt, ester or prodrug thereof.

In another aspect, the invention provides a method for reducingkinase-dependent cell growth comprising contacting a cell with a kinaseinhibitor compound as described herein or a pharmaceutically acceptableester, salt, or prodrug thereof.

In other aspects, the invention provides a method of inhibiting kinasein a subject identified as in need of such treatment, comprisingadministering a kinase inhibitor compound as described herein, or apharmaceutically acceptable ester, salt, or prodrug thereof.

In one aspect, the invention provides a kit comprising a compoundcapable of inhibiting kinase activity selected from one or more kinaseinhibitor compounds described herein, or a pharmaceutically acceptableester, salt, or prodrug thereof, and instructions for use in treatingcancer.

In one aspect, the invention provides a pharmaceutical compositioncomprising a kinase inhibitor compound as described herein, or apharmaceutically acceptable ester, salt, or prodrug thereof, togetherwith a pharmaceutically acceptable carrier.

In one aspect, the invention provides a method of synthesizing a kinaseinhibitor compound as described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates selectivity data generated using KINOMEscan® platformfor Compound 2 at 1 uM concentration and this image was generated usingTREEspot™ Software Tool.

FIG. 2 shows inhibition profiles (IC₅₀) of compounds of the inventionagainst DCLK1.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Listed below are definitions of various terms used to describe thisinvention. These definitions apply to the terms as they are usedthroughout this specification and claims, unless otherwise limited inspecific instances, either individually or as part of a larger group.

The term “alkyl,” as used herein, refers to saturated, straight- orbranched-chain hydrocarbon radicals containing, in certain embodiments,between one and six, or one and eight carbon atoms, respectively.Examples of C₁-C₆ alkyl radicals include, but are not limited to,methyl, ethyl, propyl, isopropyl, n-butyl, tert-butyl, neopentyl,n-hexyl radicals; and examples of C₁-C₈ alkyl radicals include, but arenot limited to, methyl, ethyl, propyl, isopropyl, n-butyl, tert-butyl,neopentyl, n-hexyl, heptyl, octyl radicals.

The term “alkenyl,” as used herein, denotes a monovalent group derivedfrom a hydrocarbon moiety containing, in certain embodiments, from twoto six, or two to eight carbon atoms having at least one carbon-carbondouble bond. The double bond may or may not be the point of attachmentto another group. Alkenyl groups include, but are not limited to, forexample, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, heptenyl,octenyl and the like.

The term “alkynyl,” as used herein, denotes a monovalent group derivedfrom a hydrocarbon moiety containing, in certain embodiments, from twoto six, or two to eight carbon atoms having at least one carbon-carbontriple bond. The alkynyl group may or may not be the point of attachmentto another group. Representative alkynyl groups include, but are notlimited to, for example, ethynyl, 1-propynyl, 1-butynyl, heptynyl,octynyl and the like.

The term “alkoxy” refers to an —O-alkyl radical.

The term “aryl,” as used herein, refers to a mono- or poly-cycliccarbocyclic ring system having one or more aromatic rings, fused ornon-fused, including, but not limited to, phenyl, naphthyl,tetrahydronaphthyl, indanyl, idenyl and the like.

The term “aralkyl,” as used herein, refers to an alkyl residue attachedto an aryl ring. Examples include, but are not limited to, benzyl,phenethyl and the like.

The term “cycloalkyl,” as used herein, denotes a monovalent groupderived from a monocyclic or polycyclic saturated or partially unsaturedcarbocyclic ring compound. Examples of C₃-C₈-cycloalkyl include, but notlimited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,cyclopentyl and cyclooctyl; and examples of C₃-C₁₂-cycloalkyl include,but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,bicyclo [2.2.1] heptyl, and bicyclo [2.2.2] octyl. Also contemplated area monovalent group derived from a monocyclic or polycyclic carbocyclicring compound having at least one carbon-carbon double bond by theremoval of a single hydrogen atom. Examples of such groups include, butare not limited to, cyclopropenyl, cyclobutenyl, cyclopentenyl,cyclohexenyl, cycloheptenyl, cyclooctenyl, and the like.

The term “heteroaryl,” as used herein, refers to a mono- or poly-cyclic(e.g., bi-, or tri-cyclic or more) fused or non-fused, radical or ringsystem having at least one aromatic ring, having from five to ten ringatoms of which one ring atoms is selected from S, O and N; zero, one ortwo ring atoms are additional heteroatoms independently selected from S,O and N; and the remaining ring atoms are carbon. Heteroaryl includes,but is not limited to, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl,pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl,oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl,benzimidazolyl, benzooxazolyl, quinoxalinyl, and the like.

The term “heteroaralkyl,” as used herein, refers to an alkyl residueattached to a heteroaryl ring. Examples include, but are not limited to,pyridinylmethyl, pyrimidinylethyl and the like.

The term “heterocycloalkyl,” as used herein, refers to a non-aromatic3-, 4-, 5-, 6- or 7-membered ring or a bi- or tri-cyclic group fused ofnon-fused system, where (i) each ring contains between one and threeheteroatoms independently selected from oxygen, sulfur and nitrogen,(ii) each 5-membered ring has 0 to 1 double bonds and each 6-memberedring has 0 to 2 double bonds, (iii) the nitrogen and sulfur heteroatomsmay optionally be oxidized, (iv) the nitrogen heteroatom may optionallybe quaternized, and (iv) any of the above rings may be fused to abenzene ring. Representative heterocycloalkyl groups include, but arenot limited to, [1,3]dioxolane, pyrrolidinyl, pyrazolinyl,pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl,oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl,isothiazolidinyl, and tetrahydrofuryl.

The term “alkylamino” refers to a group having the structure —NH(C₁-C₁₂alkyl) where C₁-C₁₂ alkyl is as previously defined.

The term “acyl” includes residues derived from acids, including but notlimited to carboxylic acids, carbamic acids, carbonic acids, sulfonicacids, and phosphorous acids. Examples include aliphatic carbonyls,aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphaticsulfinyls, aromatic phosphates and aliphatic phosphates. Examples ofaliphatic carbonyls include, but are not limited to, acetyl, propionyl,2-fluoroacetyl, butyryl, 2-hydroxy acetyl, and the like. In accordancewith the invention, any of the aryls, substituted aryls, heteroaryls andsubstituted heteroaryls described herein, can be any aromatic group.Aromatic groups can be substituted or unsubstituted.

The terms “halo” and “halogen,” as used herein, refer to an atomselected from fluorine, chlorine, bromine and iodine.

As described herein, compounds of the invention may optionally besubstituted with one or more substituents, such as are illustratedgenerally above, or as exemplified by particular classes, subclasses,and species of the invention. It will be appreciated that the phrase“optionally substituted” is used interchangeably with the phrase“substituted or unsubstituted.” In general, the term “substituted”,whether preceded by the term “optionally” or not, refers to thereplacement of hydrogen radicals in a given structure with the radicalof a specified substituent. Unless otherwise indicated, an optionallysubstituted group may have a substituent at each substitutable positionof the group, and when more than one position in any given structure maybe substituted with more than one substituent selected from a specifiedgroup, the substituent may be either the same or different at everyposition. The terms “optionally substituted”, “optionally substitutedalkyl,” “optionally substituted “optionally substituted alkenyl,”“optionally substituted alkynyl”, “optionally substituted cycloalkyl,”“optionally substituted cycloalkenyl,” “optionally substituted aryl”,“optionally substituted heteroaryl,” “optionally substituted aralkyl”,“optionally substituted heteroaralkyl,” “optionally substitutedheterocycloalkyl,” and any other optionally substituted group as usedherein, refer to groups that are substituted or unsubstituted byindependent replacement of one, two, or three or more of the hydrogenatoms thereon with substituents including, but not limited to:

—F, —Cl, —Br, —I,

—OH, protected hydroxy,

—NO₂, —CN,

—NH₂, protected amino, —NH—C₁-C₁₂-alkyl, —NH—C₂-C₁₂-alkenyl,—NH—C₂-C₁₂-alkenyl, —NH—C₃-C₁₂-cycloalkyl, —NH-aryl, —NH-heteroaryl,—NH-heterocycloalkyl, -dialkylamino, -diarylamino, -diheteroarylamino,

—O—C₁-C₁₂-alkyl, —O—C₂-C₁₂-alkenyl, —O—C₂-C₁₂-alkenyl,—O—C₃-C₁₂-cycloalkyl, —O-aryl, —O-heteroaryl, —O-heterocycloalkyl,

—C(O)— C₁-C₁₂-alkyl, —C(O)— C₂-C₁₂-alkenyl, —C(O)— C₂-C₁₂-alkenyl,—C(O)—C₃-C₁₂-cycloalkyl, —C(O)-aryl, —C(O)-heteroaryl,—C(O)-heterocycloalkyl,

—CONH₂, —CONH—C₁-C₁₂-alkyl, —CONH—C₂-C₁₂-alkenyl, —CONH—C₂-C₁₂-alkenyl,—CONH—C₃-C₁₂-cycloalkyl, —CONH-aryl, —CONH-heteroaryl, —CONH—heterocycloalkyl,

—OCO₂— C₁-C₁₂-alkyl, —OCO₂—C₂-C₁₂-alkenyl, —OCO₂— C₂-C₁₂-alkenyl,—OCO₂—C₃-C₁₂-cycloalkyl, —OCO₂-aryl, —OCO2-heteroaryl,—OCO₂-heterocycloalkyl, —OCONH₂, —OCONH—C₁-C₁₂-alkyl,—OCONH—C₂-C₁₂-alkenyl, —OCONH—C₂-C₁₂-alkenyl, —OCONH—C₃-C₁₂-cycloalkyl,—OCONH— aryl, —OCONH-heteroaryl, —OCONH-heterocycloalkyl,

—NHC(O)— C₁-C₁₂-alkyl, —NHC(O)—C₂-C₁₂-alkenyl, —NHC(O)—C₂-C₁₂-alkenyl,—NHC(O)—C₃-C₁₂-cycloalkyl, —NHC(O)-aryl, —NHC(O)-heteroaryl, —NHC(O)—heterocycloalkyl, —NHCO₂— C₁-C₁₂-alkyl, —NHCO₂— C₂-C₁₂-alkenyl, —NHCO₂—C₂-C₁₂-alkenyl, —NHCO₂— C₃-C₁₂-cycloalkyl, —NHCO₂— aryl,—NHCO₂-heteroaryl, —NHCO₂-heterocycloalkyl, —NHC(O)NH₂,—NHC(O)NH—C₁-C₁₂-alkyl, —NHC(O)NH—C₂-C₁₂-alkenyl,—NHC(O)NH—C₂-C₁₂-alkenyl, —NHC(O)NH—C₃-C₁₂-cycloalkyl, —NHC(O)NH-aryl,—NHC(O)NH-heteroaryl, —NHC(O)NH-heterocycloalkyl, NHC(S)NH₂,—NHC(S)NH—C₁-C₁₂-alkyl, —NHC(S)NH—C₂-C₁₂-alkenyl,—NHC(S)NH—C₂-C₁₂-alkenyl, —NHC(S)NH—C₃-C₁₂-cycloalkyl, —NHC(S)NH-aryl,—NHC(S)NH-heteroaryl, —NHC(S)NH-heterocycloalkyl, —NHC(NH)NH₂,—NHC(NH)NH—C₁-C₁₂-alkyl, —NHC(NH)NH—C₂-C₁₂-alkenyl,—NHC(NH)NH—C₂-C₁₂-alkenyl, —NHC(NH)NH—C₃-C₁₂-cycloalkyl,—NHC(NH)NH-aryl, —NHC(NH)NH-heteroaryl, —NHC(NH)NH— heterocycloalkyl,—NHC(NH)—C₁-C₁₂-alkyl, —NHC(NH)—C₂-C₁₂-alkenyl, —NHC(NH)—C₂-C₁₂-alkenyl,—NHC(NH)—C₃-C₁₂-cycloalkyl, —NHC(NH)-aryl, —NHC(NH)— heteroaryl,—NHC(NH)-heterocycloalkyl,

—C(NH)NH—C₁-C₁₂-alkyl, —C(NH)NH—C₂-C₁₂-alkenyl, —C(NH)NH—C₂-C₁₂-alkenyl,—C(NH)NH—C₃-C₁₂-cycloalkyl, —C(NH)NH-aryl, —C(NH)NH-heteroaryl,—C(NH)NH-heterocycloalkyl,

—S(O)—C₁-C₁₂-alkyl, —S(O)—C₂-C₁₂-alkenyl, —S(O)—C₂-C₁₂-alkenyl,—S(O)—C₃-C₁₂-cycloalkyl, —S(O)-aryl, —S(O)-heteroaryl,—S(O)-heterocycloalkyl —SO₂NH₂, —SO₂NH—C₁-C₁₂-alkyl,—SO₂NH—C₂-C₁₂-alkenyl, —SO₂NH—C₂-C₁₂-alkenyl, —SO₂NH—C₃-C₁₂-cycloalkyl,—SO₂NH-aryl, —SO₂NH-heteroaryl, —SO₂NH-heterocycloalkyl,—NHSO₂—C₁-C₁₂-alkyl, —NHSO₂—C₂-C₁₂-alkenyl, —NHSO₂—C₂-C₁₂-alkenyl,—NHSO₂—C₃-C₁₂-cycloalkyl, —NHSO₂-aryl, —NHSO₂-heteroaryl,—NHSO₂-heterocycloalkyl,

—CH₂NH₂, —CH₂SO₂CH₃, -aryl, -arylalkyl, -heteroaryl, -heteroarylalkyl,-heterocycloalkyl, —C₃-C₁₂-cycloalkyl, polyalkoxyalkyl, polyalkoxy,-methoxymethoxy, -methoxyethoxy, —SH, —S—C₁-C₁₂-alkyl,—S—C₂-C₁₂-alkenyl, —S—C₂-C₁₂-alkenyl, —S—C₃-C₁₂-cycloalkyl, —S-aryl,—S-heteroaryl, —S-heterocycloalkyl, or methylthiomethyl.

It is understood that the aryls, heteroaryls, alkyls, and the like canbe further substituted.

The term “cancer” includes, but is not limited to, the followingcancers: epidermoid Oral: buccal cavity, lip, tongue, mouth, pharynx;Cardiac: sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma,liposarcoma), myxoma, rhabdomyoma, fibroma, lipoma and teratoma; Lung:bronchogenic carcinoma (squamous cell or epidermoid, undifferentiatedsmall cell, undifferentiated large cell, adenocarcinoma), alveolar(bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma,chondromatous hamartoma, mesothelioma; Gastrointestinal: esophagus(squamous cell carcinoma, larynx, adenocarcinoma, leiomyosarcoma,lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas(ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoidtumors, vipoma), small bowel or small intestines (adenocarcinoma,lymphoma, carcinoid tumors, Karposi's sarcoma, leiomyoma, hemangioma,lipoma, neurofibroma, fibroma), large bowel or large intestines(adenocarcinoma, tubular adenoma, villous adenoma, hamartoma,leiomyoma), colon, colon-rectum, colorectal; rectum, Genitourinarytract: kidney (adenocarcinoma, WiIm's tumor [nephroblastoma], lymphoma,leukemia), bladder and urethra (squamous cell carcinoma, transitionalcell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma),testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma,choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma,fibroadenoma, adenomatoid tumors, lipoma); Liver: hepatoma(hepatocellular carcinoma), cholangiocarcinoma, hepatoblastoma,angiosarcoma, hepatocellular adenoma, hemangioma, biliary passages;Bone: osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibroushistiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma(reticulum cell sarcoma), multiple myeloma, malignant giant cell tumorchordoma, osteochronfroma (osteocartilaginous exostoses), benignchondroma, chondroblastoma, chondromyxofibroma, osteoid osteoma andgiant cell tumors; Nervous system: skull (osteoma, hemangioma,granuloma, xanthoma, osteitis deformans), meninges (meningioma,meningiosarcoma, gliomatosis), brain (astrocytoma, medulloblastoma,glioma, ependymoma, germinoma [pinealoma], glioblastoma multiform,oligodendroglioma, schwannoma, retinoblastoma, congenital tumors),spinal cord neurofibroma, meningioma, glioma, sarcoma); Gynecological:uterus (endometrial carcinoma), cervix (cervical carcinoma, pre-tumorcervical dysplasia), ovaries (ovarian carcinoma [serouscystadenocarcinoma, mucinous cystadenocarcinoma, unclassifiedcarcinoma], granulosa-thecal cell tumors, Sertoli-Leydig cell tumors,dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma,intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma),vagina (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma(embryonal rhabdomyosarcoma), fallopian tubes (carcinoma), breast;Hematologic: blood (myeloid leukemia [acute and chronic], acutelymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferativediseases, multiple myeloma, myelodysplastic syndrome), Hodgkin'sdisease, non-Hodgkin's lymphoma [malignant lymphoma] hairy cell;lymphoid disorders; Skin: malignant melanoma, basal cell carcinoma,squamous cell carcinoma, Karposi's sarcoma, keratoacanthoma, molesdysplastic nevi, lipoma, angioma, dermatofibroma, keloids, psoriasis,Thyroid gland: papillary thyroid carcinoma, follicular thyroidcarcinoma; medullary thyroid carcinoma, undifferentiated thyroid cancer,multiple endocrine neoplasia type 2A, multiple endocrine neoplasia type2B, familial medullary thyroid cancer, pheochromocytoma, paraganglioma;Adrenal glands: neuroblastoma, and blood-borne cancers such as chroniclymphocytic leukemia (CLL), follicular lymphoma (FL) and indolentnon-Hodgkin's lymphoma (iNHL).

Thus, the term “cancerous cell” as provided herein, includes a cellafflicted by any one of the above-identified conditions.

The term “liver disease” is damage to or disease of the liver that canlead to failure of liver functions. The term “liver disease” includes,but is not limited to, the following diseases: hepatitis, alcoholicliver disease, hereditary diseases such as hemochromatosis and Wilson'sdisease, a fatty liver disease, non-alcoholic fatty liver disease(NAFLD), non-alcoholic steatohepatitis (NASH), cirrhosis, primarybiliary cirrhosis, primary sclerosing cholangitis, Budd-Chiari syndrome,fatty liver disease resulting from hepatitis, fatty liver diseaseresulting from obesity, fatty liver disease resulting from diabetes,fatty liver disease resulting from insulin resistance, fatty liverdisease resulting from hypertriglyceridemia, Abetalipoproteinemia,glycogen storage diseases, Wolmans disease, acute fatty liver ofpregnancy, Weber-Christian disease, Gilber's syndrome, Wolmans disease,acute fatty liver of pregnancy, or lipodystrophy.

In embodiments, the disease is a neurodegenerative disease.

In some embodiments, the disease is Alzheimer's disease (AD),Parkinson's disease (PD), Huntington's (HD) diseases, amyotrophiclateral sclerosis (ALS), spinal muscular atrophy (SMA), schizophrenia,attention-deficit/hyperactivity disorder (ADHD), fetal alcohol syndromeand diabetic encephalopathy.

The term “Kinase Panel” is a list of kinases including, but not limitedto, MPS1 (TTK), ERK5 (BMK1, MAPK7), polo kinase 1,2,3, or 4, Ack1, Ack2,Abl, DCAMKL1, ABL1, Abl mutants, DCAMKL2, ARKS, BRK, MKNK2, FGFR4, TNK1,PLK1, ULK2, PLK4, PRKD1, PRKD2, PRKD3, ROS1, RPS6KA6, TAOK1, TAOK3,TNK2, Bcr-Abl, GAK, cSrc, TPR-Met, Tie2, MET, FGFR3, Aurora, Axl, Bmx,BTK, c-kit, CHK2, Flt3, MST2, p70S6K, PDGFR, PKB, PKC, Raf, ROCK-H,Rsk1, SGK, TrkA, TrkB, TrkC, AAK1, ABL1, ABL1(E255K), ABL1(F317I),ABL1(F317L), ABL1(H396P), ABL1(M351T), ABL1(Q252H), ABL1(T315I),ABL1(Y253F), ABL2, ACVR1, ACVR1B, ACVR2A, ACVR2B, ACVRL1, ADCK3, ADCK4,AKT1, AKT2, AKT3, ALK, AMPK-alpha1, AMPK-alpha2, ANKK1, ARK5, ASK1,ASK2, AURKA, AURKB, AURKC, AXL, BIKE, BLK, BMPR1A, BMPR1B, BMPR2, BMX,BRAF, BRAF(V600E), BRK, BRSK1, BRSK2, BTK, CAMK1, CAMK1D, CAMK1G,CAMK2A, CAMK2D, CAMK2G, CAMK4, CAMKK1, CAMKK2, CDC₂L1, CDC₂L2, CDK11,CDK2, CDK3, CDK5, CDK7, CDK8, CDK9, CDKL2, CDKL3, CDKL5, CHECK1, CHEK2,CIT, CLK1, CLK2, CLK3, CLK4, CSF1R, CSK, CSNK1A1L, CSNK1D, CSNK1E,CSNK1G1, CSNK1G3, CSNK2A1, CSNK2A2, CTK, DAPK1, DAPK2, DAPK3, DCAMKL1(DLCK1), DCAMKL2 (DCLK2), DCAMKL3, DDR1, DDR2, DLK, DMPK, DMPK2, DRAK1,DRAK2, DYRK1A, DYRK1B, DYRK2, EGFR, EGFR (E746-A750DEL), EGFR (G719C),EGFR (G719S), EGFR(L747-E749del, A750P), EGFR(L747-S752del, P753S),EGFR(L747-T751del,Sins), EGFR(L858R), EGFR(L858R,T790M), EGFR(L861Q),EGFR(S752-1759del), EPHAL EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7,EPHA8, EPHB1, EPHB2, EPHB3, EPHB4, EPHB6, ERBB2, ERBB3, ERBB4, ERK1,ERK2, ERK3, ERK4, ERK5, ERK8, ERN1, FAK, FER, FES, FGFR1, FGFR2, FGFR3,FGFR3(G697C), FGFR4, FGR, FLT1, FLT3, FLT3(D835H), FLT3(D835Y),FLT3(ITD), FLT3(K663Q), FLT3(N841I), FLT4, FRK, FYN, GAK,GCN2(Kin.Dom.2,S808G), GRK1, GRK4, GRK7, GSK3A, GSK3B, HCK, HIPK1,HIPK2, HIPK3, HIPK4, HPK1, HUNK, ICK, IGF1R, IKK-ALPHA, IKK-BETA,IKK-EPSILON, INSR, INSRR, IRAK1, IRAK3, ITK, JAK1(JH1domain-catalytic),JAK1(JH2domain-pseudokinase), JAK2(JH1domain-catalytic),JAK3(JH1domain-catalytic), JNK1, JNK2, JNK3, KIT, KIT(D816V),KIT(L576P), KIT(V559D), KIT(V559D,T670I), KIT(V559D,V654A), LATS1,LATS2, LCK, LIMK1, LIMK2, LKB1, LOK, LTK, LYN, LZK, MAK, MAP3K1,MAP2K15, MAP3K2, MAP3K3, MAP3K4, MAP4K2, MAP4K3, MAP4K5, MAPKAPK2,MAPKAPK5, MARK1, MARK2, MARK3, MARK4, MAST1, MEK1, MEK2, MEK3, MEK4,MEK6, MELK, MERTK, MET, MET(M1250T), MET(Y1235D), MINK, MKNK1, MKNK2,MLCK, MLK1, MLK2, MLK3, MRCKA, MRCKB, MST1, MST1R, MST2, MST3, MST4,MUSK, MYLK, MYLK2, MYO3A, MYO3B, NDR1, NDR2, NEK1, NEK2, NEK5, NEK6,NEK7, NEK9, NIM1, NLK, OSR1, p38-alpha, p38-beta, p38-delta, p38-gamma,PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PCTK1, PCTK2, PCTK3, PDGFRA, PDGFRB,PDPK1, PFTAIRE2, PFTK1, PHKG1, PHKG2, PIK3C2B, PIK3C2G, PIK3CA,PIK3CA(C420R), PIK3CA(E542K), PIK3CA(E545A), PIK3CA(E545K),PIK3CA(H1047L), PIK3CA(H1047Y), PIK3CA(M1043I), PIK3CA(Q546K), PIK3CB,PIK3CD, PIK3CG, PIK4CB, PIM1, PIM2, PIM3, PIP5K1A, PIP5K2B, PKAC-ALPHA,PKAC-BETA, PKMYT1, PKN1, PKN2, PLK1, PLK2, PLK3, PLK4, PRKCD, PRKCE,PRKCH, PRKCQ, PRKD1, PRKD3, PRKG1, PRKG2, PRKR, PRKX, PRP4, PYK2, QSK,RAF1, RET, RET(M918T), RET(V804L), RET(V804M), RIOK1, RIOK2, RIOK3,RIPK1, RIPK2, RIPK4, ROCK1, ROCK2, ROS1, RPS6KA1(Kin.Dom.1-N-terminal),RPS6KA1(Kin.Dom.2-C-terminal), RPS6KA2(Kin.Dom.1-N-terminal),RPS6KA2(Kin.Dom.2-C-terminal), RPS6KA3(Kin.Dom.1-N-terminal),RPS6KA4(Kin.Dom.1-N-terminal), RPS6KA4(Kin.Dom.2-C-terminal),RPS6KA5(Kin.Dom.1-N-terminal), RPS6KA5(Kin.Dom.2-C-terminal),RPS6KA6(Kin.Dom.1-N-terminal), RPS6KA6(Kin.Dom.2-C-terminal), SBK1,SgK085, SgK110, SIK, SIK2, SLK, SNARK, SRC, SRMS, SRPK1, SRPK2, SRPK3,STK16, STK33, STK39, SYK, TAK1, TAO1, TAOK2, TAOK3, TBK1, TEC, TESK1,TGFBR1, TGFBR2, TIE1, TIE2, TLK1, TLK2, TNIK, TNK1, TNK2, TNNI3K, TRKA,TRKB, TRKC, TSSK1B, TTK, TXK, TYK2(JH1domain-catalytic),TYK2(JH2domain-pseudokinase), TYRO3, ULK1, ULK2, ULK3, VEGFR2, WEE1,WEE2, YANK2, YANK3, YES, YSK1, YSK4, ZAK and ZAP70. Compounds of theinvention are screened against the kinase panel (wild type and/ormutation thereof) and inhibit the activity of at least one of said panelmembers.

Mutant forms of a kinase means single or multiple amino acid changesfrom the wild-type sequence.

The term “subject” as used herein refers to a mammal. A subjecttherefore refers to, for example, dogs, cats, horses, cows, pigs, guineapigs, and the like. Preferably the subject is a human. When the subjectis a human, the subject may be referred to herein as a patient.

“Treat”, “treating” and “treatment” refer to a method of alleviating orabating a disease and/or its attendant symptoms.

As used herein, the term “pharmaceutically acceptable salt” refers tothose salts of the compounds formed by the process of the presentinvention which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswithout undue toxicity, irritation, allergic response and the like, andare commensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, S. M. Berge, etal. describes pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 66: 1-19 (1977). The salts can be prepared insitu during the final isolation and purification of the compounds of theinvention, or separately by reacting the free base function with asuitable organic acid. Examples of pharmaceutically acceptable include,but are not limited to, nontoxic acid addition salts are salts of anamino group formed with inorganic acids such as hydrochloric acid,hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid orwith organic acids such as acetic acid, maleic acid, tartaric acid,citric acid, succinic acid or malonic acid or by using other methodsused in the art such as ion exchange. Other pharmaceutically acceptablesalts include, but are not limited to, adipate, alginate, ascorbate,aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate,camphorate, camphorsulfonate, citrate, cyclopentanepropionate,digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate,glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate,hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate,lactate, laurate, lauryl sulfate, malate, maleate, malonate,methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate,oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate,phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate,tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts,and the like. Representative alkali or alkaline earth metal saltsinclude sodium, lithium, potassium, calcium, magnesium, and the like.Further pharmaceutically acceptable salts include, when appropriate,nontoxic ammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and arylsulfonate.

As used herein, the term “pharmaceutically acceptable ester” refers toesters of the compounds formed by the process of the present inventionwhich hydrolyze in vivo and include those that break down readily in thehuman body to leave the parent compound or a salt thereof. Suitableester groups include, for example, those derived from pharmaceuticallyacceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic,cycloalkanoic and alkanedioic acids, in which each alkyl or alkenylmoiety advantageously has not more than 6 carbon atoms. Examples ofparticular esters include, but are not limited to, formates, acetates,propionates, butyrates, acrylates and ethylsuccinates.

The term “pharmaceutically acceptable prodrugs” as used herein refers tothose prodrugs of the compounds formed by the process of the presentinvention which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of humans and lower animalswith undue toxicity, irritation, allergic response, and the like,commensurate with a reasonable benefit/risk ratio, and effective fortheir intended use, as well as the zwitterionic forms, where possible,of the compounds of the present invention. “Prodrug”, as used hereinmeans a compound which is convertible in vivo by metabolic means (e.g.by hydrolysis) to afford any compound delineated by the formulae of theinstant invention. Various forms of prodrugs are known in the art, forexample, as discussed in Bundgaard, (ed.), Design of Prodrugs, Elsevier(1985); Widder, et al. (ed.), Methods in Enzymology, vol. 4, AcademicPress (1985); Krogsgaard-Larsen, et al., (ed). “Design and Applicationof Prodrugs, Textbook of Drug Design and Development, Chapter 5, 113-191(1991); Bundgaard, et al., Journal of Drug Deliver Reviews,8:1-38(1992); Bundgaard, J. of Pharmaceutical Sciences, 77:285 et seq.(1988); Higuchi and Stella (eds.) Prodrugs as Novel Drug DeliverySystems, American Chemical Society (1975); and Bernard Testa & JoachimMayer, “Hydrolysis In Drug And Prodrug Metabolism: Chemistry,Biochemistry And Enzymology,” John Wiley and Sons, Ltd. (2002).

This invention also encompasses pharmaceutical compositions containing,and methods of treating disorders through administering,pharmaceutically acceptable prodrugs of compounds of the invention. Forexample, compounds of the invention having free amino, amido, hydroxy orcarboxylic groups can be converted into prodrugs. Prodrugs includecompounds wherein an amino acid residue, or a polypeptide chain of twoor more (e.g., two, three or four) amino acid residues is covalentlyjoined through an amide or ester bond to a free amino, hydroxy orcarboxylic acid group of compounds of the invention. The amino acidresidues include but are not limited to the 20 naturally occurring aminoacids commonly designated by three letter symbols and also includes4-hydroxyproline, hydroxyysine, demosine, isodemosine,3-methylhistidine, norvalin, beta-alanine, gamma-aminobutyric acid,citrulline, homocysteine, homoserine, ornithine and methionine sulfone.Additional types of prodrugs are also encompassed. For instance, freecarboxyl groups can be derivatized as amides or alkyl esters. Freehydroxy groups may be derivatized using groups including but not limitedto hemisuccinates, phosphate esters, dimethylaminoacetates, andphosphoryloxymethyloxy carbonyls, as outlined in Advanced Drug DeliveryReviews, 1996, 19, 1 15. Carbamate prodrugs of hydroxy and amino groupsare also included, as are carbonate prodrugs, sulfonate esters andsulfate esters of hydroxy groups. Derivatization of hydroxy groups as(acyloxy)methyl and (acyloxy)ethyl ethers wherein the acyl group may bean alkyl ester, optionally substituted with groups including but notlimited to ether, amine and carboxylic acid functionalities, or wherethe acyl group is an amino acid ester as described above, are alsoencompassed. Prodrugs of this type are described in J. Med. Chem. 1996,39, 10. Free amines can also be derivatized as amides, sulfonamides orphosphonamides. All of these prodrug moieties may incorporate groupsincluding but not limited to ether, amine and carboxylic acidfunctionalities

Combinations of substituents and variables envisioned by this inventionare only those that result in the formation of stable compounds. Theterm “stable”, as used herein, refers to compounds which possessstability sufficient to allow manufacture and which maintains theintegrity of the compound for a sufficient period of time to be usefulfor the purposes detailed herein (e.g., therapeutic or prophylacticadministration to a subject).

Doublecortin-Like Kinases

Described herein are compounds that can inhibit at least one ofdoublecortin-like kinases (DCLK), e.g., isoforms such as DCLK1 andDCLK2, which are members of serine/threonine-protein kinase family andCa²⁺/calmodulin-dependent protein kinase class of enzymes.

These doublecortin-like kinases (DCLK) commonly contain i) twoN-terminal doublecortin domains, which can bind or associatemicrotubules; ii) a C-terminal serine/threonine protein kinase domain,which shows substantial homology to Ca²⁺/calmodulin-dependent proteinkinase, and iii) a serine/proline-rich domain in between thedoublecortin and the protein kinase domains, which mediates multipleprotein-protein interactions.

Human serine/threonine-protein kinase doublecortin-like kinase 1 (DCLK1)refers to the protein products of the human gene DCLK1. This includesany serine/threonine-protein kinases (EC:2.7.11.1) referred to as, forexample, doublecortin and CaM kinase-like 1(DCAMKL1), doublecortindomain-containing protein 3A(DCDC₃A), CPG16 (candidate plasticity gene16), CaMK-like CREB regulatory kinase 1 (CL1, CLICK-I, CLICK1, or CLIK1)and/or KIAA0369, proteins listed under UNIPROT ID: Q5VZY9 or uniprot ID:O15075, or homologous proteins or isoforms thereof, including but notlimited to isoforms 1-4 (alternate nomenclature DCLK1-long,DCLK1-short).

Likewise, human serine/threonine-protein kinase doublecortin-like kinase2 (DCLK2) refers to the protein products of the human gene DCLK2. Thisincludes any serine/threonine-protein kinases (EC:2.7.11.1) which may bealternately named as, for example, CaMK-like CREB regulatory kinase 2(CL2, CLICK-II, CLICK2, or CLIK2); doublecortin and CaM kinase-like 2(DCAMKL2); doublecortin domain-containing protein 3B (DCDC₃B);doublecortin-like and CAM kinase-like 2 (DCLK2); doublecortin-likekinase 2 (DCK2); serine/threonine-protein kinase DCLK2 and proteinslisted under UNIPROT ID: Q8N568, or homologous proteins or isoformsthereof. Isoforms include but are not limited to isoforms 1-3 listed inUNIPROT.

DCLK1 is a microtubule-associated protein that plays a key role inneuronal migration, retrograde transport, neuronal apoptosis,neurogenesis and synapse maturation by regulation of mitotic spindleformation, which can be independent from its protein kinase activity(Reiner, O. et al, BMC Genomics 2006, 7 (1), 1-16).

Moreover, DCLK1 is frequently mutated across many cancer types. Inparticular, DCLK1 can be a driver gene for gastic cancer and is listedamong the top 15 presumed driver genes (The Cancer Genome AtlasResearch, Nature 2014, 513 (7517), 202-209). Expression of DCLK1 is alsoassociated with poor prognosis in gastric cancer patients (Győrffy, B.et al., PLoS ONE 2013, 8 (12)). Additionally, DCLK1 can be a marker ofquiescent stem-cells in the stomach, intestine and pancreas, and thosecells have been shown to function as the cancer stem cells whichinitiate and support cancers in the intestine and pancreas, alone, orwhen harboring oncogenic mutations, or upon loss of tumour suppressorgenes. For instance, ablation of these cells induces rapid regression oftumors in murine models of intestinal cancer (Ito, H. et al., PLoS ONE2016, 11 (1); Nakanishi, Y. et al., Nature genetics 2013, 45 (1),98-103; Westphalen, C. B., et. al, The Journal of clinical investigation2014, 124 (3), 1283-95; Westphalen, C. B. et al., Cell Stem Cell 18 (4),441-455).

Accordingly, as described herein, DCLK1/2 positive cells and DCLK1/2functions can be targeted as promising therapeutic strategies in cancertreatments (e.g. treatments for gastric, pancreatic and intestinalcancers).

However, currently available DCLK1/2 kinase inhibitors are highlymulti-targeted and have been shown to inhibit a number of other kinasesand bromodomains. Prior to the invention described herein, there were nopotent or selective inhibitors of the DCLK1/2 kinases described in theliterature.

Accordingly, described herein are series of compounds based around apyrimido-diazepinone scaffold. Such compounds, including those based ona2-amino-5,8,11-trimethyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-onescaffold, can be potent and selective inhibitors of DCLK1 or DCLK2, oralternatively, selective dual inhibitors of DCLK1 and DCLK2, therebyproviding a method of treating/preventing a related disease mediated byDCLK1 and/or DCLK2.

DCLK1/2 Inhibitor Compounds

Described herein are series of compounds based around apyrimido-diazepinone scaffold. Such compounds can be inhibitors ofkinases (e.g., DCLK, including DCLK isoforms such as DCLK1 and/or DCLK2)and are referred to herein as “DCLK1/2 inhibitor compounds.”

In embodiments, the invention provides a compound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₅ is hydrogen, optionally substituted alkyl, optionally substitutedaralkyl, or optionally substituted carbocyclic; and

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In embodiments, R₅ is methyl.

In embodiments, R₂ is unsubstituted alkyl.

In certain embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, eachof which may be optionally substituted with one or more halogen.

In certain embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In embodiments, p is 0; or when p is 1, R₇ is unsubstituted alkyl.

In certain embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In another embodiment, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkoxy, CO₂Me,

In embodiments, R₁ is phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl,pyrazolyl, imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each ofwhich may be optionally substituted.

In embodiments, R₁ is substituted with 0-4 substituents, selected fromhalo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)), CO₂H,C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)), C(O)N(R_(A))(R_(A)),alkyl, aryl, arylalkyl, alkoxy, heteroaryl, heterocyclic, carbocyclic,SO₂(R_(A)), SO₃(R_(A)), SO₂N(R_(A))(R_(A)), SO₂NH(R_(A)), SO₂NH₂,PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each of which may be furthersubstituted, and wherein each R_(A) is independently selected fromalkyl, alkenyl, carbocyclic, aryl, heteroaryl, and heterocyclic, or twoR_(A) on the same atom combine to form a heterocyclic, each of which maybe further substituted.

In certain embodiments, R₁ is selected from the group consisting of

In embodiments, the compound is of formula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted.

In embodiments, R₂ is unsubstituted alkyl.

In certain embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, eachof which may be optionally substituted with one or more halogen.

In certain embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In certain embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In another embodiment, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;wherein each R_(A) is independently selected from alkyl, alkenyl,carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A) on thesame atom combine to form a heterocyclic, each of which may be furthersubstituted.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkoxy, CO₂Me,

In embodiments, R₁ is phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl,pyrazolyl, imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each ofwhich may be optionally substituted.

In embodiments, R₁ is substituted with 0-4 substituents, selected fromhalo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)), CO₂H,C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)), C(O)N(R_(A))(R_(A)),alkyl, aryl, arylalkyl, alkoxy, heteroaryl, heterocyclic, carbocyclic,SO₂(R_(A)), SO₃(R_(A)), SO₂N(R_(A)) (R_(A)), SO₂NH(R_(A)), SO₂NH₂,PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each of which may be furthersubstituted, and wherein each R_(A) is independently selected fromalkyl, alkenyl, carbocyclic, aryl, heteroaryl, and heterocyclic, or twoR_(A) on the same atom combine to form a heterocyclic, each of which maybe further substituted.

In embodiments, R₁ is selected from the group consisting of

In embodiments, the compound is of formula F-1-b:

or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, R₂ is unsubstituted alkyl.

In certain embodiments, R₂ is methyl, ethyl, propyl, or iso-propyl, eachof which may be optionally substituted with one or more halogen such asF.

In certain embodiments, R₂ is —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃.

In certain embodiments, R′ is selected from alkoxy, CO₂Me,

In certain embodiments, q is 1 or 2.

In certain embodiments, when q is 2, one R′ is —OCH₃.

In embodiments, the compound has the structure of any one of Compounds1-21 as described herein, or a pharmaceutically acceptable salt, esteror prodrug thereof.

In embodiments, the compound has a structure selected from the groupconsisting of:

or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, the compound has a structure according to formula A-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

X is CHR₄, CR₄, NH, NR₄ or N;

Y is NR₅, N, S, SO, SO₂, O, CHR₅, or CR₅; wherein at least one of X andY is NH, NR₄, NR₅, N, S, SO, SO₂, or O;

A is a single bond or double bond;

B is a single bond or double bond, wherein both A and B are not doublebonds;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₄ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

or R₃ and X, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted;

or X and Y, together with the atoms to which they are attached, form a3-8 membered carbocyclic, aryl, heterocyclic, or heteroaryl; each ofwhich is optionally substituted; and

R₆ is hydrogen or optionally substituted alkyl.

In certain embodiments, the invention provides a compound wherein X isCR₄ or CHR₄, and Y is NR₅.

In other embodiments, the invention provides a compound wherein R₄ ishydrogen, alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, each ofwhich may be optionally substituted; and R₅ is hydrogen, alkyl, aryl,heteroaryl, heterocyclic, or carbocyclic, each of which may beoptionally substituted.

In certain embodiments, the invention provides a compound wherein X andY, together with the atoms to which they are attached, form a 3-8membered cycloalkyl, aryl, heterocycloalkyl, or heteroaryl; each ofwhich is optionally substituted.

In other embodiments, the invention provides a compound wherein R₃ andX, together with the atoms to which they are attached, form a 3-8membered cycloalkyl, aryl, heterocycloalkyl, or heteroaryl; each ofwhich is optionally substituted.

In some embodiments, the invention provides a compound wherein X is Nand Y is CR₅.

In a further embodiment, R₅ is alkyl, aryl, heteroaryl, heterocyclic, orcarbocyclic, each of which may be optionally substituted.

In embodiments, the invention provides a compound of B-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is aryl, or heteroaryl, wherein R₁ may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen or methyl;

R₄ is hydrogen or methyl; and

R₆ is hydrogen.

In one embodiment, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In a further embodiment, R₁ is substituted with 0-4 substituents,selected from N(R_(A))(R_(A)), C(O)NH(R_(A)), alkoxy, and heterocyclic,each of which may be further substituted; wherein each R_(A) isindependently selected from alkyl, and heterocyclic.

-   -   In another further embodiment, R₁ is substituted with 0-4        substituents, selected from alkoxy,

In embodiments, the invention provides a compound of formula C-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is aryl, heteroaryl, which may be optionally substituted;

R₂ is hydrogen or methyl;

R₃ is hydrogen;

R₄ is hydrogen; and

R₆ is hydrogen.

In certain embodiments, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In a further embodiment, R₁ is substituted with 0-4 substituents,selected from alkoxy, or heterocyclic, which may be further substituted.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkoxy,

In embodiments, the invention provides a compound of formula D-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-6.

In one embodiment, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is alkyl, phenyl, cyclohexyl, piperidinyl,quinolinyl, or pyridyl, each of which may be optionally substituted.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from halo, nitro, cyano, hydroxyl, amino, NH(R_(A)),N(R_(A))(R_(A)), CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;wherein each R_(A) is independently selected from alkyl, carbocyclic,aryl, heteroaryl, and heterocyclic.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkyl, alkoxy, hydroxyl,

In embodiments, the invention provides a compound of formula E-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-6.

In certain embodiments, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In another further embodiment, R₁ is substituted with 0-4 substituents,selected from halo, nitro, cyano, hydroxyl, amino, NH(R_(A)),N(R_(A))(R_(A)), CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;wherein each R_(A) is independently selected from alkyl, carbocyclic,aryl, heteroaryl, and heterocyclic.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkoxy,

In embodiments, the invention provides a compound of formula F-I-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

Y is S, SO, SO₂, or O;

R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic, wherein R₁may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₆ is hydrogen or optionally substituted alkyl;

each R₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and

p is 0-4.

In one embodiment, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is phenyl or pyridyl, each of which may beoptionally substituted.

In another embodiment, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, and carbocyclic, each of which may be further substituted;

wherein each R_(A) is independently selected from alkyl, carbocyclic,aryl, heteroaryl, and heterocyclic.

In a further embodiment, R₁ is substituted with 0-4 substituents,selected from alkoxy, CO₂Me,

In embodiments, the invention provides a compound of formula G-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₁ is alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3 heteroatomsselected from O, S, or N; or R₁ is aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, wherein R₁ may be optionally substituted;

R₂ is hydrogen or optionally substituted alkyl;

R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted;

R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted; and

R₆ is hydrogen or optionally substituted alkyl.

In one embodiment, R₁ is methyl, ethyl, propyl, iso-propyl, butyl,s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl, pyrrolidino,phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl, pyrazinyl,pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl, isoxazolyl,pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl, each of whichmay be optionally substituted.

In a further embodiment, R₁ is optionally substituted phenyl.

In another embodiment, R₁ is substituted with 0-4 substituents, selectedfrom halo, nitro, cyano, hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)),CO₂H, C(O)R_(A), C(O)NH₂, C(O)NH(R_(A)), C(O)N(R_(A))(R_(A)), alkyl,aryl, arylalkyl, alkoxy, heteroaryl, heterocyclic, and carbocyclic, eachof which may be further substituted; wherein each R_(A) is independentlyselected from alkyl, carbocyclic, aryl, heteroaryl, and heterocyclic.

In certain embodiments, R₁ is substituted with 0-4 substituents,selected from alkoxy, hydroxyl,

In another embodiment, R₅ is optionally substituted phenyl or optionallysubstituted cyclopentyl.

In embodiments, the invention provides a compound of formula I-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

A is a single bond or double bond;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent (for example, halogen, —OH, —NO₂, —CN,—NH₂, protected amino, —NH—C₁-C₁₂-alkyl, —NH—C₂-C₁₂-alkenyl,—NH—C₂-C₁₂-alkenyl, —NH—C₃-C₁₂-cycloalkyl, —NH-aryl, —NH-heteroaryl,—NH-heterocycloalkyl, -dialkylamino, -diarylamino, -diheteroarylamino,—O—C₁-C₁₂-alkyl, —O-C₂-C₁₂-alkenyl, —O—C₂-C₁₂-alkenyl,—O—C₃-C₁₂-cycloalkyl, —O-aryl, —O-heteroaryl, —O-heterocycloalkyl,—C(O)—C₁-C₁₂-alkyl, —C(O)—C₂-C₁₂-alkenyl, —C(O)—C₂-C₁₂-alkenyl,—C(O)—C₃-C₁₂-cycloalkyl, —C(O)-aryl, —C(O)-heteroaryl,—C(O)-heterocycloalkyl, —CONH₂, —CONH—C₁-C₁₂-alkyl,—CONH—C₂-C₁₂-alkenyl, —CONH—C₂-C₁₂-alkenyl, —CONH—C₃-C₁₂-cycloalkyl,—CONH-aryl, —CONH-heteroaryl, —CONH-heterocycloalkyl, —OCO₂—C₁-C₁₂-alkyl, —OCO₂—C₂-C₁₂-alkenyl, —OCO₂—C₂-C₁₂-alkenyl,—OCO2-C₃-C₁₂-cycloalkyl, —OCO₂-aryl, —OCO₂-heteroaryl,—OCO₂-heterocycloalkyl, —OCONH₂, —OCONH—C₁-C₁₂-alkyl,OCONH—C₂-C₁₂-alkenyl, —OCONH—C₂-C₁₂-alkenyl, —OCONH—C₃-C₁₂-cycloalkyl,—OCONH-aryl, —OCONH-heteroaryl, —OCONH-heterocycloalkyl,—NHC(O)—C₁-C₁₂-alkyl, —NHC(O)—C₂-C₁₂-alkenyl, —NHC(O)—C₂-C₁₂-alkenyl,—NHC(O)—C₃-C₁₂-cycloalkyl, —NHC(O)-aryl, —NHC(O)-heteroaryl,—NHC(O)-heterocycloalkyl, —NHCO₂—C₁-C₁₂-alkyl, —NHCO₂—C₂-C₁₂-alkenyl,—NHCO₂— C₂-C₁₂-alkenyl, —NHCO₂—C₃-C₁₂-cycloalkyl, —NHCO₂-aryl,—NHCO₂-heteroaryl, —NHCO₂-heterocycloalkyl, —NHC(O)NH₂,—NHC(O)NH—C₁-C₁₂-alkyl, —NHC(O)NH—C₂-C₁₂-alkenyl,—NHC(O)NH—C₂-C₁₂-alkenyl, —NHC(O)NH—C₃-C₁₂-cycloalkyl, —NHC(O)NH-aryl,—NHC(O)NH-heteroaryl, —NHC(O)NH-heterocycloalkyl, NHC(S)NH₂,—NHC(S)NH-C₁-C₁₂-alkyl, —NHC(S)NH—C₂-C₁₂-alkenyl,—NHC(S)NH—C₂-C₁₂-alkenyl, —NHC(S)NH—C₃-C₁₂-cycloalkyl, —NHC(S)NH-aryl,—NHC(S)NH-heteroaryl, —NHC(S)NH-heterocycloalkyl, —NHC(NH)NH₂,—NHC(NH)NH—C₁-C₁₂-alkyl, —NHC(NH)NH—C₂-C₁₂-alkenyl,—NHC(NH)NH—C₂-C₁₂-alkenyl, —NHC(NH)NH—C₃-C₁₂-cycloalkyl,—NHC(NH)NH-aryl, —NHC(NH)NH-heteroaryl, —NHC(NH)NH— heterocycloalkyl,—NHC(NH)—C₁-C₁₂-alkyl, —NHC(NH)—C₂-C₁₂-alkenyl, —NHC(NH)—C₂-C₁₂-alkenyl,—NHC(NH)—C₃-C₁₂-cycloalkyl, —NHC(NH)-aryl, —NHC(NH)— heteroaryl,—NHC(NH)-heterocycloalkyl, —C(NH)NH—C₁-C₁₂-alkyl,—C(NH)NH-C₂-C₁₂-alkenyl, —C(NH)NH—C₂-C₁₂-alkenyl,—C(NH)NH—C₃-C₁₂-cycloalkyl, —C(NH)NH-aryl, —C(NH)NH-heteroaryl,—C(NH)NH-heterocycloalkyl, —S(O)—C₁-C₁₂-alkyl, —S(O)—C₂-C₁₂-alkenyl,—S(O)—C₂-C₁₂-alkenyl, —S(O)—C₃-C₁₂-cycloalkyl, —S(O)-aryl, —S(O)—heteroaryl, —S(O)-heterocycloalkyl —SO₂NH₂, —SO₂NH—C₁-C₁₂-alkyl,—SO₂NH—C₂-C₁₂-alkenyl, —SO₂NH—C₂-C₁₂-alkenyl, —SO₂NH—C₃-C₁₂-cycloalkyl,—SO₂NH-aryl, —SO₂NH-heteroaryl, —SO₂NH-heterocycloalkyl,—NHSO₂—C₁-C₁₂-alkyl, —NHSO₂—C₂-C₁₂-alkenyl, —NHSO₂—C₂-C₁₂-alkenyl,—NHSO₂—C₃-C₁₂-cycloalkyl, —NHSO₂-aryl, —NHSO₂-heteroaryl,—NHSO₂-heterocycloalkyl, —CH₂NH₂, —CH₂SO₂CH₃, aryl, arylalkyl,heteroaryl, heteroarylalkyl, heterocycloalkyl, —C₃-C₁₂-cycloalkyl,polyalkoxyalkyl, polyalkoxy, -methoxymethoxy, -methoxyethoxy, —SH,—S—C₁-C₁₂-alkyl, —S—C₂-C₁₂-alkenyl, —S—C₂-C₁₂-alkenyl,—S—C₃-C₁₂-cycloalkyl, —S-aryl, —S— heteroaryl, —S-heterocycloalkyl, ormethylthiomethyl);

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl (including aralkyl),optionally substituted cycloalkyl, and optionally substitutedheterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of formula II-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

E is NR₂ or CHR₂;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl (including aralkyl), optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In certain embodiments, E is NR₂. In certain embodiments, R₂ is H or—CH₃.

In embodiments, the invention provides a compound of formula III-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl (including aralkyl), optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of formula IV-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl (including aralkyl), optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of formula V-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,

wherein,

R₂ is hydrogen or optionally substituted alkyl;

R₃ is —OH or —O-(optionally substituted alkyl);

R₄ is hydrogen or optionally substituted alkyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of Formula VI-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; or

two X moieties on adjacent atoms of the thiophene ring can form,together with the atoms to which they are attached, a phenyl ring; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of Formula VII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of Formula VIII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

X is an optional substituent as defined for formula I;

Z is O or S;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and

R₆ is hydrogen or optionally substituted alkyl.

In embodiments, the invention provides a compound of Formula IX-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein,

A is a single bond or double bond;

R′ is H or alkyl;

L is absent, S, SO, SO₂, or CO;

Y is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl;

R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted;

R₂ and R₂′ are each independently hydrogen, optionally substitutedalkyl, optionally substituted cycloalkyl, and optionally substitutedheterocyclyl;

or Y and R₂′ can form, together with the atoms to which they areattached, a five-membered ring; and

R₆ is hydrogen or optionally substituted alkyl.

Exemplary methods for preparation or synthesizing of these compounds aredescribed herein and in, e.g., International Publication Nos.WO2010/080712 and WO2014145909, each of which is incorporated byreference in its entirety.

Another embodiment is a method of making a compound of any of theformulae herein using any one, or combination of, reactions delineatedherein. The method can include the use of one or more intermediates orchemical reagents delineated herein.

Another aspect is an isotopically labeled compound of any of theformulae delineated herein. Such compounds have one or more isotopeatoms which may or may not be radioactive (e.g., ³H, ²H, ¹⁴C, ¹³C, ³⁵S,³²P, ¹²⁵I, and ¹³¹I) introduced into the compound. Such compounds areuseful for drug metabolism studies and diagnostics, as well astherapeutic applications.

A compound of the invention can be prepared as a pharmaceuticallyacceptable acid addition salt by reacting the free base form of thecompound with a pharmaceutically acceptable inorganic or organic acid.Alternatively, a pharmaceutically acceptable base addition salt of acompound of the invention can be prepared by reacting the free acid formof the compound with a pharmaceutically acceptable inorganic or organicbase.

Alternatively, the salt forms of the compounds of the invention can beprepared using salts of the starting materials or intermediates.

The free acid or free base forms of the compounds of the invention canbe prepared from the corresponding base addition salt or acid additionsalt from, respectively. For example, a compound of the invention in anacid addition salt form can be converted to the corresponding free baseby treating with a suitable base (e.g., ammonium hydroxide solution,sodium hydroxide, and the like). A compound of the invention in a baseaddition salt form can be converted to the corresponding free acid bytreating with a suitable acid (e.g., hydrochloric acid, etc.).

Prodrug derivatives of the compounds of the invention can be prepared bymethods known to those of ordinary skill in the art (e.g., for furtherdetails see Saulnier et al., (1994), Bioorganic and Medicinal ChemistryLetters, Vol. 4, p. 1985). For example, appropriate prodrugs can beprepared by reacting a non-derivatized compound of the invention with asuitable carbamylating agent (e.g., 1,1-acyloxyalkylcarbanochloridate,para-nitrophenyl carbonate, or the like).

Protected derivatives of the compounds of the invention can be made bymeans known to those of ordinary skill in the art. A detaileddescription of techniques applicable to the creation of protectinggroups and their removal can be found in T. W. Greene, “ProtectingGroups in Organic Chemistry”, 3rd edition, John Wiley and Sons, Inc.,1999.

Compounds of the present invention can be conveniently prepared, orformed during the process of the invention, as solvates (e.g.,hydrates). Hydrates of compounds of the present invention can beconveniently prepared by recrystallization from an aqueous/organicsolvent mixture, using organic solvents such as dioxin, tetrahydrofuranor methanol.

Acids and bases useful in the methods herein are known in the art. Acidcatalysts are any acidic chemical, which can be inorganic (e.g.,hydrochloric, sulfuric, nitric acids, aluminum trichloride) or organic(e.g., camphorsulfonic acid, p-toluenesulfonic acid, acetic acid,ytterbium triflate) in nature. Acids are useful in either catalytic orstoichiometric amounts to facilitate chemical reactions. Bases are anybasic chemical, which can be inorganic (e.g., sodium bicarbonate,potassium hydroxide) or organic (e.g., triethylamine, pyridine) innature. Bases are useful in either catalytic or stoichiometric amountsto facilitate chemical reactions.

In addition, some of the compounds of this invention have one or moredouble bonds, or one or more asymmetric centers. Such compounds canoccur as racemates, racemic mixtures, single enantiomers, individualdiastereomers, diastereomeric mixtures, and cis- or trans- or E- orZ-double isomeric forms, and other stereoisomeric forms that may bedefined, in terms of absolute stereochemistry, as (R)- or (S)-, or as(D)- or (L)- for amino acids. All such isomeric forms of these compoundsare expressly included in the present invention. Optical isomers may beprepared from their respective optically active precursors by theprocedures described above, or by resolving the racemic mixtures. Theresolution can be carried out in the presence of a resolving agent, bychromatography or by repeated crystallization or by some combination ofthese techniques which are known to those skilled in the art. Furtherdetails regarding resolutions can be found in Jacques, et al.,Enantiomers, Racemates, and Resolutions (John Wiley & Sons, 1981). Thecompounds of this invention may also be represented in multipletautomeric forms, in such instances, the invention expressly includesall tautomeric forms of the compounds described herein (e.g., alkylationof a ring system may result in alkylation at multiple sites, theinvention expressly includes all such reaction products). When thecompounds described herein contain olefinic double bonds or othercenters of geometric asymmetry, and unless specified otherwise, it isintended that the compounds include both E and Z geometric isomers.Likewise, all tautomeric forms are also intended to be included. Theconfiguration of any carbon-carbon double bond appearing herein isselected for convenience only and is not intended to designate aparticular configuration unless the text so states; thus a carbon-carbondouble bond depicted arbitrarily herein as trans may be cis, trans, or amixture of the two in any proportion. All such isomeric forms of suchcompounds are expressly included in the present invention. All crystalforms of the compounds described herein are expressly included in thepresent invention.

The synthesized compounds can be separated from a reaction mixture andfurther purified by a method such as column chromatography, highpressure liquid chromatography, or recrystallization. As can beappreciated by the skilled artisan, further methods of synthesizing thecompounds of the formulae herein will be evident to those of ordinaryskill in the art. Additionally, the various synthetic steps may beperformed in an alternate sequence or order to give the desiredcompounds. In addition, the solvents, temperatures, reaction durations,etc. delineated herein are for purposes of illustration only and one ofordinary skill in the art will recognize that variation of the reactionconditions can produce the desired bridged macrocyclic products of thepresent invention. Synthetic chemistry transformations and protectinggroup methodologies (protection and deprotection) useful in synthesizingthe compounds described herein are known in the art and include, forexample, those such as described in R. Larock, Comprehensive OrganicTransformations, VCH Publishers (1989); T. W. Greene and P.G.M. Wuts,Protective Groups in Organic Synthesis, 2d. Ed., John Wiley and Sons(1991); L. Fieser and M. Fieser, Fieser and Fieser's Reagents forOrganic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed.,Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons(1995), and subsequent editions thereof.

The compounds of this invention may be modified by appending variousfunctionalities via any synthetic means delineated herein to enhanceselective biological properties. Such modifications are known in the artand include those which increase biological penetration into a givenbiological system (e.g., blood, lymphatic system, central nervoussystem), increase oral availability, increase solubility to allowadministration by injection, alter metabolism and alter rate ofexcretion.

The compounds of the invention are defined herein by their chemicalstructures and/or chemical names. Where a compound is referred to byboth a chemical structure and a chemical name, and the chemicalstructure and chemical name conflict, the chemical structure isdeterminative of the compound's identity.

The recitation of a listing of chemical groups in any definition of avariable herein includes definitions of that variable as any singlegroup or combination of listed groups. The recitation of an embodimentfor a variable herein includes that embodiment as any single embodimentor in combination with any other embodiments or portions thereof.

Methods

In one aspect, the invention provides a method of treating a disease ina subject mediated by a kinase that is doublecortin-like kinase(DCLK1/2) comprising administering to the subject a DCLK inhibitorcompound (e.g. compound of formula F-1, F-1-a, F-1-b of A-1) asdescribed herein, or a pharmaceutically acceptable salt, ester orprodrug thereof. For instance, the DCLK inhibitor compound mayselectively inhibit DCLK1 and/or DCLK2, with inhibition constant (Ki)for inhibiting DCLK1 and/or DCLK2 less than about 1 μM, less than about500 nM, less than about 100 nM, less than about 50 nM, less than about40 nM, less than about 30 nM, less than about 20 nM, or preferably, lessthan about 15 nM.

In another aspect, the invention provides a method for reducingdoublecortin-like kinase (DCLK1/2)-dependent cell growth comprisingcontacting a cell with a DCLK inhibitor compound as described herein, ora pharmaceutically acceptable salt, ester or prodrug thereof.

In another aspect, the invention provides a method of inhibiting adoublecortin-like kinase (DCLK1/2) in a subject identified as in need ofsuch treatment, comprising administering a DCLK inhibitor compound asdescribed herein, or a pharmaceutically acceptable salt, ester orprodrug thereof.

In embodiments, the invention provides a method of inhibiting a disease,wherein the disease is mediated by DCLK1. In one embodiment, theinvention provides a method of inhibiting a disease, wherein the diseaseis mediated by DCLK2. In one embodiment, the invention provides a methodof inhibiting a disease, wherein the disease is mediated by DCLK1 andDCLK2.

In another embodiment, the invention provides a method of inhibiting adisease, wherein the disease is cancer or a proliferation disease.

In some embodiments, the cancer is lung cancer, colon cancer, breastcancer, prostate cancer, liver cancer, brain cancer, kidney cancer,ovarian cancer, stomach cancer, skin cancer, bone cancer, gastriccancer, pancreatic cancer, glioma, hepatocellular carcinoma, papillaryrenal carcinoma, head and neck squamous cell carcinoma, leukemia,lymphoma, myeloma, or a solid tumor.

In some embodiments, the cancer is a blood-borne cancer (e.g., chroniclymphocytic leukemia (CLL), follicular lymphoma (FL) or indolentnon-Hodgkin's lymphoma (iNHL)). In an embodiment, the cancer is chroniclymphocytic leukemia (CLL), follicular lymphoma (FL), or indolentnon-Hodgkin's lymphoma (iNHL).

In some embodiments, the cancer is pertinent to gastic organs,gastrointestinal tract, or digestive organs including stomach, smallintestine, large intestine, tongue, salivary glands, pancreas, liver,and gallbladder.

In some embodiments, the disease is Barretts' esophagus, esophagealcancer, salivary gland malignancies, colon and colorectal cancer,intestinal cancer, gastric cancer, pancreatic cancer, skin cancer orneuroblastoma.

In some embodiments, the invention includes a method of reducingrecurrence and/or relapse of the cancer or proliferation disease asdescribed herein.

In some embodiments, the invention includes a method of reducingmigration and/or metathesis of the cancer or proliferation disease asdescribed herein.

In some embodiments, the invention includes a method of treating,reducing or preventing resistant cancer cells and/or cancer stem cellsin patients suffered from or diagnosed with the cancer or proliferationdisease as described herein.

In embodiments, the disease is a liver disease.

In some embodiments, the disease is a fatty liver disease, non-alcoholicfatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH),cirrhosis, fatty liver disease resulting from hepatitis, fatty liverdisease resulting from obesity, fatty liver disease resulting fromdiabetes, fatty liver disease resulting from insulin resistance, fattyliver disease resulting from hypertriglyceridemia, Abetalipoproteinemia,glycogen storage diseases, Wolmans disease, or acute fatty liver ofpregnancy.

In embodiments, the disease is a neurodegenerative disease.

In some embodiments, the disease is Alzheimer's disease (AD),Parkinson's disease (PD), Huntington's (HD) diseases, amyotrophiclateral sclerosis (ALS), spinal muscular atrophy (SMA), schizophrenia,attention-deficit/hyperactivity disorder (ADHD), fetal alcohol syndromeand diabetic encephalopathy.

In another aspect, the invention provides a method of treating a kinasemediated disorder in a subject comprising: administering to the subjectidentified as in need thereof a kinase inhibitor compound as describedherein, or a pharmaceutically acceptable salt, ester or prodrug thereof.

In embodiments, a compound described herein is an inhibitor of DCLK1. Inembodiments, a compound described herein is an inhibitor of DCLK2. Inembodiments, a compound described herein is a selective inhibitor ofDCLK1. In embodiments, a compound described herein is a selectiveinhibitor of DCLK2. In embodiments, a compound described herein is adual inhibitor of DCLK1 and DCLK2. In embodiments, a compound describedherein is a selective dual inhibitor of DCLK1 and DCLK2.

In embodiments, the subject is administered an additional therapeuticagent. In some embodiments, an additional therapeutic agent is ananti-inflammatory agent. In some embodiments, an additional therapeuticagent is a chemotherapy agent. In some embodiments, an additionaltherapeutic agent is a monoclonal antibody. In some embodiment, anadditional therapeutic agent is a therapeutic agent for liver disease.In some embodiments, an additional therapeutic agent is a therapeuticagent for neurodegenerative disease.

In a further embodiment, the compound and the additional therapeuticagent are administered simultaneously or sequentially.

In another aspect, the invention provides a method for reducingkinase-dependent cell growth comprising contacting a cell with a kinaseinhibitor compound as described herein.

In other aspects, the invention provides a method of inhibiting kinasein a subject identified as in need of such treatment, comprisingadministering a kinase inhibitor compound as described herein.

In embodiments, the invention provides a method wherein the subject is ahuman.

In other embodiments, the invention provides a method wherein the kinaseinhibitor has a Ki for inhibiting DCLK1 and/or DCLK2 less than about 1μM, less than about 500 nM, less than about 100 nM, less than about 50nM, less than about 40 nM, less than about 30 nM, less than about 20 nM,or less than about 15 nM.

In one embodiment, the invention provides a method of synthesizing akinase inhibitor compound as described herein. For example, thecompounds (e.g. compounds of formulae F-1, F-1-a and F-1-b) can besynthesized as described herein (e.g., Schemes 1-4 in Examples).

Another aspect of this invention provides compounds or compositions thatare inhibitors of protein kinases (e.g., DCLK, including DCLK1 and/orDCLK2), and thus are useful for the treatment of the diseases,disorders, and conditions, along with other uses described herein. Incertain embodiments, these compositions optionally further comprise oneor more additional therapeutic agents.

As inhibitors of protein kinases (e.g., DCLK, including DCLK1 and/orDCLK2), the compounds and compositions of this invention areparticularly useful for treating or lessening the severity of a disease,condition, or disorder where a protein kinase is implicated in thedisease, condition, or disorder.

In one aspect, the present invention provides a method for treating orlessening the severity of a disease, condition, or disorder where aprotein kinase is implicated in the disease state. In another aspect,the present invention provides a method for treating or lessening theseverity of a kinase disease, condition, or disorder where inhibition ofenzymatic activity is implicated in the treatment of the disease. Inanother aspect, this invention provides a method for treating orlessening the severity of a disease, condition, or disorder withcompounds that inhibit enzymatic activity by binding to the proteinkinase. Another aspect provides a method for treating or lessening theseverity of a kinase disease, condition, or disorder by inhibitingenzymatic activity of the kinase with a protein kinase inhibitor.

In some embodiments, said method is used to treat or prevent a conditionselected from autoimmune diseases, inflammatory diseases, cancers,tumors, malignant tumors, proliferative and hyperproliferative diseases,immunologically-mediated diseases, bone diseases, metabolic diseases,neurological and neurodegenerative diseases, cardiovascular diseases,liver disease, hormone related diseases, allergies, asthma, andneurodegenerative diseases including Alzheimer's disease. In otherembodiments, said condition is selected from a proliferative disorder,liver disease and a neurodegenerative disorder.

One aspect of this invention provides compounds that are useful for thetreatment of diseases, disorders, and conditions characterized byexcessive or abnormal cell proliferation. Such diseases include, aproliferative or hyperproliferative disease, cancer, liver disease and aneurodegenerative disease. Examples of proliferative andhyperproliferative diseases include, without limitation, cancer.

The term “cancer” includes, but is not limited to, the followingcancers: breast; ovary; cervix; prostate; testis, genitourinary tract;esophagus; larynx, glioblastoma; neuroblastoma; stomach; skin,keratoacanthoma; lung, epidermoid carcinoma, large cell carcinoma, smallcell carcinoma, lung adenocarcinoma; bone; colon; colorectal; adenoma;pancreas, adenocarcinoma; thyroid, follicular carcinoma,undifferentiated carcinoma, papillary carcinoma; seminoma; melanoma;sarcoma; bladder carcinoma; liver carcinoma and biliary passages; kidneycarcinoma; myeloid disorders; lymphoid disorders, Hodgkin's, hairycells; buccal cavity and pharynx (oral), lip, tongue, mouth, pharynx;small intestine; colon-rectum, large intestine, rectum, brain andcentral nervous system; chronic myeloid leukemia (CML), and leukemia.

In some embodiments, the compounds of this invention are useful fortreating cancer, such as colorectal, thyroid, breast, and lung cancer;and myeloproliferative disorders, such as polycythemia vera,thrombocythemia, myeloid metaplasia with myelofibrosis, chronicmyelogenous leukemia, chronic myelomonocytic leukemia, hypereosinophilicsyndrome, juvenile myelomonocytic leukemia, and systemic mast celldisease.

In some embodiments, the compounds of this invention are useful fortreating hematopoietic disorders, in particular, acute-myelogenousleukemia (AMLi), chronic-myelogenous leukemia (CML), acute-promyelocyticleukemia, and acute lymphocytic leukemia (ALL).

In some embodiments, the compounds of this invention are useful fortreating a cancer or proliferative disease pertinent to gastic organs,gastrointestinal tract, and digestive organs including the stomach,small intestine, large intestine, tongue, salivary glands, pancreas,liver, and gallbladder.

In some embodiments, the compounds of this invention are useful fortreating Barretts' esophagus, esophageal cancer, salivary glandmalignancies, colon and colorectal cancer, intestinal cancer, gastriccancer, pancreatic cancer, skin cancer and neuroblastoma.

One aspect of this invention provides compounds that are useful for thetreatment of diseases, disorders, and damages in liver.

In some embodiments, the compounds of this invention are useful fortreating a fatty liver disease, non-alcoholic fatty acid liver disease(NAFLD), non-alcoholic steatohepatitis (NASH), fatty liver diseaseresulting from hepatitis, fatty liver disease resulting from obesity,fatty liver disease resulting from diabetes, fatty liver diseaseresulting from insulin resistance, fatty liver disease resulting fromhypertriglyceridemia, Abetalipoproteinemia, glycogen storage diseases,Weber-Christian disease, Wolmans disease, acute fatty liver ofpregnancy, or lipodystrophy.

One aspect of this invention provides compounds that are useful for thetreatment of a neurodegenerative disease.

In some embodiments, the disease is Alzheimer's disease (AD),Parkinson's disease (PD), Huntington's (HD) diseases, amyotrophiclateral sclerosis (ALS), spinal muscular atrophy (SMA), schizophrenia,attention-deficit/hyperactivity disorder (ADHD), fetal alcohol syndromeand diabetic encephalopathy.

Another aspect of this invention provides a method for the treatment orlessening the severity of a disease selected from a cancer, aproliferative or hyperproliterative disease, a liver disease, or aneurodegenerative disease, comprising administering an effective amountof a compound, or a pharmaceutically acceptable composition comprising acompound, to a subject in need thereof.

As inhibitors of protein kinases, the compounds and compositions of thisinvention are also useful in biological samples. One aspect of theinvention relates to inhibiting protein kinase activity in a biologicalsample, which method comprises contacting said biological sample with acompound of the invention or a composition comprising said compound. Theterm “biological sample”, as used herein, means an in vitro or an exvivo sample, including, without limitation, cell cultures or extractsthereof, biopsied material obtained from a mammal or extracts thereof;and blood, saliva, urine, feces, semen, tears, or other body fluids orextracts thereof. Inhibition of protein kinase activity in a biologicalsample is useful for a variety of purposes that are known to one ofskill in the art. Examples of such purposes include, but are not limitedto, blood transfusion, organ-transplantation, and biological specimenstorage.

Another aspect of this invention relates to the study of protein kinasesin biological and pathological phenomena; the study of intracellularsignal transduction pathways mediated by such protein kinases; and thecomparative evaluation of new protein kinase inhibitors. Examples ofsuch uses include, but are not limited to, biological assays such asenzyme (e.g. kinetics, binding and inhibition) assays, gel shift assays(electrophoretic mobility shift assay) and cell-based assays.

The activity of the compounds as protein kinase inhibitors may beassayed in vitro, in vivo or in a cell line. In vitro assays includeassays that determine inhibition of either the kinase activity or ATPaseactivity of the activated kinase. Alternate in vitro assays quantitatethe ability of the inhibitor to bind to the protein kinase and may bemeasured either by radiolabelling the inhibitor prior to binding,isolating the inhibitor/kinase complex and determining the amount ofradiolabel bound, or by running a competition experiment where newinhibitors are incubated with the kinase bound to known radioligands.Preferably, in vitro assays quantitate the ability of the inhibitor tobind to the protein kinase and may be measured either by probing theinhibitor with fluorescent molecules prior to binding, isolating theinhibitor/kinase complex and determining the amount of the bound probes,utilization of a mobility shift assay with substrates treated ornon-treated with protein kinase, for example, in the presence of ATPplus inhibitor or DMSO control, or by running a competition experimentwhere new inhibitors are incubated with the kinase bound to knownfluorescent probes.

Detailed conditions for assaying a compound utilized in this inventionas an inhibitor of various kinases are set forth in the Examples below.

In accordance with the foregoing, the present invention further providesa method for preventing or treating any of the diseases or disordersdescribed above in a subject in need of such treatment, which methodcomprises administering to said subject a therapeutically effectiveamount of a compound of the invention or a pharmaceutically acceptablesalt thereof. For any of the above uses, the required dosage will varydepending on the mode of administration, the particular condition to betreated and the effect desired.

Pharmaceutical Compositions

In another aspect, the invention provides a pharmaceutical compositioncomprising a kinase inhibitor compound (e.g. DCLK1/2) as describedherein, or a pharmaceutically acceptable ester, salt, or prodrugthereof, together with a pharmaceutically acceptable carrier.

Compounds of the invention can be administered as pharmaceuticalcompositions by any conventional route, in particular enterally, e.g.,orally, e.g., in the form of tablets or capsules, or parenterally, e.g.,in the form of injectable solutions or suspensions, topically, e.g., inthe form of lotions, gels, ointments or creams, or in a nasal orsuppository form. Pharmaceutical compositions comprising a compound ofthe present invention in free form or in a pharmaceutically acceptablesalt form in association with at least one pharmaceutically acceptablecarrier or diluent can be manufactured in a conventional manner bymixing, granulating or coating methods. For example, oral compositionscan be tablets or gelatin capsules comprising the active ingredienttogether with a) diluents, e.g., lactose, dextrose, sucrose, mannitol,sorbitol, cellulose and/or glycine; b) lubricants, e.g., silica, talcum,stearic acid, its magnesium or calcium salt and/or polyethyleneglycol;for tablets also c) binders, e.g., magnesium aluminum silicate, starchpaste, gelatin, tragacanth, methylcellulose, sodiumcarboxymethylcellulose and or polyvinylpyrrolidone; if desired d)disintegrants, e.g., starches, agar, alginic acid or its sodium salt, oreffervescent mixtures; and/or e) absorbents, colorants, flavors andsweeteners. Injectable compositions can be aqueous isotonic solutions orsuspensions, and suppositories can be prepared from fatty emulsions orsuspensions. The compositions may be sterilized and/or containadjuvants, such as preserving, stabilizing, wetting or emulsifyingagents, solution promoters, salts for regulating the osmotic pressureand/or buffers. In addition, they may also contain other therapeuticallyvaluable substances. Suitable formulations for transdermal applicationsinclude an effective amount of a compound of the present invention witha carrier. A carrier can include absorbable pharmacologically acceptablesolvents to assist passage through the skin of the host. For example,transdermal devices are in the form of a bandage comprising a backingmember, a reservoir containing the compound optionally with carriers,optionally a rate controlling barrier to deliver the compound to theskin of the host at a controlled and predetermined rate over a prolongedperiod of time, and means to secure the device to the skin. Matrixtransdermal formulations may also be used. Suitable formulations fortopical application, e.g., to the skin and eyes, are preferably aqueoussolutions, ointments, creams or gels well-known in the art. Such maycontain solubilizers, stabilizers, tonicity enhancing agents, buffersand preservatives.

Compounds of the invention can be administered in therapeuticallyeffective amounts in combination with one or more therapeutic agents(pharmaceutical combinations). For example, synergistic effects canoccur with other immunomodulatory or anti-inflammatory substances, forexample when used in combination with cyclosporin, rapamycin, orascomycin, or immunosuppressant analogues thereof, for examplecyclosporin A (CsA), cyclosporin G, FK-506, rapamycin, or comparablecompounds, corticosteroids, cyclophosphamide, azathioprine,methotrexate, brequinar, leflunomide, mizoribine, mycophenolic acid,mycophenolate mofetil, 15-deoxyspergualin, immunosuppressant antibodies,especially monoclonal antibodies for leukocyte receptors, for exampleMHC, CD2, CD3, CD4, CD7, CD25, CD28, B7, CD45, CD58 or their ligands, orother immunomodulatory compounds, such as CTLA41g. Where the compoundsof the invention are administered in conjunction with other therapies,dosages of the co-administered compounds will of course vary dependingon the type of co-drug employed, on the specific drug employed, on thecondition being treated and so forth.

The pharmaceutical compositions of the present invention comprise atherapeutically effective amount of a compound of the present inventionformulated together with one or more pharmaceutically acceptablecarriers. As used herein, the term “pharmaceutically acceptable carrier”means a non-toxic, inert solid, semi-solid or liquid filler, diluent,encapsulating material or formulation auxiliary of any type. Thepharmaceutical compositions of this invention can be administered tohumans and other animals orally, rectally, parenterally,intracisternally, intravaginally, intraperitoneally, topically (as bypowders, ointments, or drops), buccally, or as an oral or nasal spray.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups andelixirs. In addition to the active compounds, the liquid dosage formsmay contain inert diluents commonly used in the art such as, forexample, water or other solvents, solubilizing agents and emulsifierssuch as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethylacetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butyleneglycol, dimethylformamide, oils (in particular, cottonseed, groundnut,corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can also include adjuvants such as wetting agents,emulsifying and suspending agents, sweetening, flavoring, and perfumingagents.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions may be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation may also be a sterile injectablesolution, suspension or emulsion in a nontoxic parenterally acceptablediluent or solvent, for example, as a solution in 1,3-butanediol. Amongthe acceptable vehicles and solvents that may be employed are water,Ringer's solution, U.S.P. and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or diglycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This may be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolutionwhich, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform is accomplished by dissolving or suspending the drug in an oilvehicle.

Compositions for rectal or vaginal administration are preferablysuppositories which can be prepared by mixing the compounds of thisinvention with suitable non-irritating excipients or carriers such ascocoa butter, polyethylene glycol or a suppository wax which are solidat ambient temperature but liquid at body temperature and therefore meltin the rectum or vaginal cavity and release the active compound.

Solid compositions of a similar type may also be employed as fillers insoft and hard-filled gelatin capsules using such excipients as lactoseor milk sugar as well as high molecular weight polyethylene glycols andthe like.

The active compounds can also be in micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active compound may be admixed with at least one inertdiluent such as sucrose, lactose or starch. Such dosage forms may alsocomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may also comprisebuffering agents.

Dosage forms for topical or transdermal administration of a compound ofthis invention include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants or patches. The active componentis admixed under sterile conditions with a pharmaceutically acceptablecarrier and any needed preservatives or buffers as may be required.Ophthalmic formulation, ear drops, eye ointments, powders and solutionsare also contemplated as being within the scope of this invention.

The ointments, pastes, creams and gels may contain, in addition to anactive compound of this invention, excipients such as animal andvegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulosederivatives, polyethylene glycols, silicones, bentonites, silicic acid,talc and zinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to the compounds of thisinvention, excipients such as lactose, talc, silicic acid, aluminumhydroxide, calcium silicates and polyamide powder, or mixtures of thesesubstances. Sprays can additionally contain customary propellants suchas chlorofluorohydrocarbons.

Transdermal patches have the added advantage of providing controlleddelivery of a compound to the body. Such dosage forms can be made bydissolving or dispensing the compound in the proper medium. Absorptionenhancers can also be used to increase the flux of the compound acrossthe skin. The rate can be controlled by either providing a ratecontrolling membrane or by dispersing the compound in a polymer matrixor gel.

According to the methods of treatment of the present invention,disorders are treated or prevented in a subject, such as a human orother animal, by administering to the subject a therapeuticallyeffective amount of a compound of the invention, in such amounts and forsuch time as is necessary to achieve the desired result. The term“therapeutically effective amount” of a compound of the invention, asused herein, means a sufficient amount of the compound so as to decreasethe symptoms of a disorder in a subject. As is well understood in themedical arts a therapeutically effective amount of a compound of thisinvention will be at a reasonable benefit/risk ratio applicable to anymedical treatment.

In general, compounds of the invention will be administered intherapeutically effective amounts via any of the usual and acceptablemodes known in the art, either singly or in combination with one or moretherapeutic agents. A therapeutically effective amount may vary widelydepending on the severity of the disease, the age and relative health ofthe subject, the potency of the compound used and other factors. Ingeneral, satisfactory results are indicated to be obtained systemicallyat daily dosages of from about 0.03 to 2.5 mg/kg per body weight. Anindicated daily dosage in the larger mammal, e.g. humans, is in therange from about 0.5 mg to about 100 mg, conveniently administered, e.g.in divided doses up to four times a day or in retard form. Suitable unitdosage forms for oral administration comprise from ca. 1 to 50 mg activeingredient.

In certain embodiments, a therapeutic amount or dose of the compounds ofthe present invention may range from about 0.1 mg/Kg to about 500 mg/Kg,alternatively from about 1 to about 50 mg/Kg. In general, treatmentregimens according to the present invention comprise administration to apatient in need of such treatment from about 10 mg to about 1000 mg ofthe compound(s) of this invention per day in single or multiple doses.Therapeutic amounts or doses will also vary depending on route ofadministration, as well as the possibility of co-usage with otheragents.

Upon improvement of a subject's condition, a maintenance dose of acompound, composition or combination of this invention may beadministered, if necessary. Subsequently, the dosage or frequency ofadministration, or both, may be reduced, as a function of the symptoms,to a level at which the improved condition is retained when the symptomshave been alleviated to the desired level, treatment should cease. Thesubject may, however, require intermittent treatment on a long-termbasis upon any recurrence of disease symptoms.

It will be understood, however, that the total daily usage of thecompounds and compositions of the present invention will be decided bythe attending physician within the scope of sound medical judgment. Thespecific inhibitory dose for any particular patient will depend upon avariety of factors including the disorder being treated and the severityof the disorder; the activity of the specific compound employed; thespecific composition employed; the age, body weight, general health, sexand diet of the patient; the time of administration, route ofadministration, and rate of excretion of the specific compound employed;the duration of the treatment; drugs used in combination or coincidentalwith the specific compound employed; and like factors well known in themedical arts.

The invention also provides for a pharmaceutical combinations, e.g. akit, comprising a) a first agent which is a kinase inhibitor compound asdisclosed herein, in free form or in pharmaceutically acceptable saltform, and b) at least one co-agent. The kit can comprise instructionsfor its administration.

The terms “co-administration” or “combined administration” or the likeas utilized herein are meant to encompass administration of the selectedtherapeutic agents to a single patient, and are intended to includetreatment regimens in which the agents are not necessarily administeredby the same route of administration or at the same time.

The term “pharmaceutical combination” as used herein means a productthat results from the mixing or combining of more than one activeingredient and includes both fixed and non-fixed combinations of theactive ingredients. The term “fixed combination” means that the activeingredients, e.g. a compound of the invention and a co-agent, are bothadministered to a patient simultaneously in the form of a single entityor dosage. The term “non-fixed combination” means that the activeingredients, e.g. a compound of the invention and a co-agent, are bothadministered to a patient as separate entities either simultaneously,concurrently or sequentially with no specific time limits, wherein suchadministration provides therapeutically effective levels of the twocompounds in the body of the patient. The latter also applies tococktail therapy, e.g. the administration of three or more activeingredients.

In certain embodiments, these compositions optionally further compriseone or more additional therapeutic agents. For example, chemotherapeuticagents or other antiproliferative agents may be combined with thecompounds of this invention to treat proliferative diseases and cancer.Examples of known chemotherapeutic agents include, but are not limitedto, Gleevec™, adriamycin, dexamethasone, vincristine, cyclophosphamide,fluorouracil, topotecan, taxol, interferons, and platinum derivatives.

Other examples of agents the compounds of this invention may also becombined with include, without limitation: treatments for Alzheimer'sDisease such as Aricept18 and Excelon®; treatments for Parkinson'sDisease such as L-DOPA/carbidopa, entacapone, ropinrole, pramipexole,bromocriptine, pergolide, trihexephendyl, and amantadine; agents fortreating Multiple Sclerosis (MS) such as beta interferon (e.g., Avonex®and Rebif®), Copaxone®, and mitoxantrone; treatments for asthma such asalbuterol and Singulair®; agents for treating schizophrenia such aszyprexa, risperdal, seroquel, and haloperidol; anti-inflammatory agentssuch as corticosteroids, TNF blockers, IL-I RA, azathioprine,cyclophosphamide, and sulfasalazine; immunomodulatory andimmunosuppressive agents such as cyclosporin, tacrolimus, rapamycin,mycophenolate mofetil, interferons, corticosteroids, cyclophophamide,azathioprine, and sulfasalazine; neurotrophic factors such asacetylcholinesterase inhibitors, MAO inhibitors, interferons,anti-convulsants, ion channel blockers, riluzole, and antiparkinsonianagents; agents for treating cardiovascular disease such asbeta-blockers, ACE inhibitors, diuretics, nitrates, calcium channelblockers, and statins; agents for treating liver disease such ascorticosteroids, cholestyramine, interferons, and anti-viral agents;agents for treating blood disorders such as corticosteroids,antileukemic agents, and growth factors; and agents for treatingimmunodeficiency disorders such as gamma globulin. Some examples ofmaterials which can serve as pharmaceutically acceptable carriersinclude, but are not limited to, ion exchangers, alumina, aluminumstearate, lecithin, serum proteins, such as human serum albumin, buffersubstances such as phosphates, glycine, sorbic acid, or potassiumsorbate, partial glyceride mixtures of saturated vegetable fatty acids,water, salts or electrolytes, such as protamine sulfate, disodiumhydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zincsalts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone,polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, woolfat, sugars such as lactose, glucose and sucrose; starches such as cornstarch and potato starch; cellulose and its derivatives such as sodiumcarboxymethyl cellulose, ethyl cellulose and cellulose acetate; powderedtragacanth; malt; gelatin; talc; excipients such as cocoa butter andsuppository waxes, oils such as peanut oil, cottonseed oil; saffloweroil; sesame oil; olive oil; corn oil and soybean oil; glycols; such apropylene glycol or polyethylene glycol; esters such as ethyl oleate andethyl laurate, agar; buffering agents such as magnesium hydroxide andaluminum hydroxide; alginic acid; pyrogen-free water, isotonic saline;Ringer's solution; ethyl alcohol, and phosphate buffer solutions, aswell as other non-toxic compatible lubricants such as sodium laurylsulfate and magnesium stearate, as well as coloring agents, releasingagents, coating agents, sweetening, flavoring and perfuming agents,preservatives and antioxidants can also be present in the composition,according to the judgment of the formulator. The protein kinaseinhibitors or pharmaceutical salts thereof may be formulated intopharmaceutical compositions for administration to animals or humans.These pharmaceutical compositions, which comprise an amount of theprotein inhibitor effective to treat or prevent a proteinkinase-mediated condition and a pharmaceutically acceptable carrier, areanother embodiment of the present invention.

In another aspect, the invention provides a kit comprising a compoundcapable of inhibiting kinase activity selected from one or more of thekinase inhibitor compounds described herein, and instructions for use intreating cancer.

EXAMPLES

The compounds and processes of the present invention will be betterunderstood in connection with the following examples, which are intendedas an illustration only and not to limit the scope of the invention.Various changes and modifications to the disclosed embodiments will beapparent to those skilled in the art and such changes and modificationsincluding, without limitation, those relating to the chemicalstructures, substituents, derivatives, formulations and/or methods ofthe invention may be made without departing from the spirit of theinvention and the scope of the appended claims.

Abbreviations

DCLK1, doublecortin like kinase 1.

DCLK2, doublecortin like kinase 2.

Ni-NTA, nickel-nitrilotriacetic acid

FAM, fluorescein amidite

HTS, high-throughput screening

HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid

DTT, dithiothreitol

EDTA, ethylenediaminetetraacetic acid

Chemistry General Methods

Unless otherwise noted, reagents and solvents were obtained fromcommercial suppliers and were used without further purification. ¹H NMRspectra were recorded on a 500 MHz Bruker Avance III spectrometer andchemical shifts are reported in parts per million (ppm, δ) downfieldfrom tetramethylsilane (TMS). Coupling constants (J) are reported in Hz.Spin multiplicities are described as s (singlet), br (broad singlet), d(doublet), t (triplet), q (quartet), and m (multiplet). Mass spectrawere obtained on a Waters Acquity I UPLC. Preparative HPLC was performedon a Waters Sunfire C18 column (19 mm×50 mm, 5 μM) using a gradient of15-95% methanol in water containing 0.05% trifluoroacetic acid (TFA)over 22 min (28 min run time) at a flow rate of 20 mL/min. Assayedcompounds were isolated and tested as TFA salts. Purities of assayedcompounds were in all cases greater than 95%, as determined byreverse-phase HPLC analysis.

Synthesis

i. Scheme 1: Synthesis of Compound 1

Compound 1 can be synthesized using the following scheme 1.

In Scheme 1, ethyl2-((2-chloro-5-nitropyrimidin-4-yl)(methyl)amino)benzoate (2) can besynthesized as follows: A mixture of ethyl 2-(methylamino)benzoate (1.44g, 8.0 mmol), diisopropylethylamine (DIEA) (2.8 mL, 16.0 mmol) and2,4-dichloro-5-nitropyrimidine (2.30 g, 12.0 mmol) in dioxane (40 mL)was heated at 50° C. for 6 hours. After the reaction was complete asmonitored by thin layer chromatography (TLC), the reaction solution wasconcentrated and the residue was purified by silica-gel columnchromatography with ethyl acetate and hexane (1/20, v/v) to give thetitle compound (2.51 g, 93%). ¹H NMR (600 MHz, CDCl3) δ 8.44 (s, 1H),8.02 (d, J=7.2 Hz, 1H), 7.59 (t, J=7.2 Hz, 1H), 7.44 (t, J=7.2 Hz, 1H),7.22 (d, J=7.8 Hz, 1H), 4.28-4.18 (m, 2H), 3.58 (s, 3H), 1.29 (t, J=7.2Hz, 3H). ¹³C NMR (150 MHz, CDCl3) δ 164.4, 160.8, 157.0, 155.2, 142.8,134.1, 132.5, 128.9, 127.7, 61.6, 42.0, 14.0. MS (ESI) m/z 337 (M+H)⁺

In Scheme 1,2-chloro-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(3) can be synthesized as follows:

A mixture of (2) (2.35 g, 6.98 mmol) and iron power (3.9 g, 69.8 mmol)in acetic acid (100 mL) was heated at 50° C. for 9 hours. After thereaction was complete as monitored by reverse phase analyticalliquid-chromatography electrospray mass spectrometry (LC-MS), the excessof iron was removed and the mixture was concentrated in vacuo. Theresulting residue was poured into ice-water which resulted in a solidprecipitate that was collected by filtration, washed with water and airdried to give the title compound (1.55 g, 85%). ¹H NMR (600 MHz,DMSO-d6) δ 10.44 (s, 1H), 8.14 (s, 1H), 7.72 (d, J=4.8 Hz, 1H), 7.58 (s,1H), 7.27 (d, J=6.0 Hz, 1H), 7.21 (s, 1H), 3.33 (s, 3H). ¹³C NMR (150MHz, DMSO-d6) δ 167.6, 161.4, 153.4, 149.7, 147.9, 134.2, 132.0, 125.9,124.6, 124.3, 120.1, 37.2. MS (ESI) m/z 261 (M+H)⁺

In Scheme 1,2-chloro-5,11-dimethyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(4) can be synthesized as follows:

To a stirred suspension of (3) 688 mg, 2.64 mmol) and Met (0.25 mL, 4.0mmol) in dimethyl acetamide (DMA, 40.0 mL) was added NaH (360 mg, 60%suspension in mineral oil) at −10° C. and the reaction was graduallywarmed to 0° C. After the reaction was complete as monitored by LC-MS,the solution was poured into ice-water which resulted in a solidprecipitate. The precipitate was collected by filtration, washed withwater and air dried to give the title compound (563 mg, 77%). ¹H NMR(600 MHz, DMSO-d6) δ 8.57 (s, 1H), 7.68 (dd, J=1.2, 7.2 Hz, 1H),7.54-7.51 (m, 1H), 7.25 (d, J=7.8 Hz, 1H), 7.20-7.18 (m, 1H), 3.41 (s,3H), 3.32 (s, 3H). ¹³C NMR (150 MHz, DMSO-d6) δ 167.1, 163.8, 153.7,153.4, 148.6, 133.5, 132.4, 128.7, 126.0, 124.6, 118.9, 38.1, 36.4. MS(ESI) m/z 275 (M+H)⁺.

In Scheme 1,2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)-5,11-dimethyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(XMD8-85-1, or Compound 1) can be synthesized as follows:

A mixture of (4) (26 mg, 0.1 mmol),2-methoxy-4-(4-methylpiperizin-1-yl)benzamine (22 mg, 0.1 mmol), X-Phos(4.3 mg), Pd₂(dba)₃ (5.5 mg) and K₂CO₃ (41.5 mg, 0.3 mmol) in 1.2 mL oft-BuOH was heated at 100° C. in a seal tube for 4 h. Then the reactionwas filtered through celite and eluted with dichloromethane. Thedichloromethane was removed in vacuo and the resulting crude product waspurified by reverse-phase prep-HPLC using a water (0.05%TFA)/acetonitrile (0.05% TFA) gradient to afford the compounds as TFAsalt (20 mg, yield: 36%). ¹H NMR (600 MHz, CD3OD) δ 7.83 (dd, J=1.2, 7.8Hz, 1H), 7.71 (s, 1H), 7.62-7.59 (m, 2H), 7.30 (d, J=8.4 Hz, 1H), 7.26(t, J=7.2 Hz, 1H), 6.75 (d, J=1.8 Hz, 1H), 6.66 (d, J=7.2 Hz, 1H),3.92-3.87 (m, 5H), 3.66-3.60 (m, 2H), 3.49 (s, 3H), 3.30-3.24 (m, 2H),3.14-3.08 (m, 2H), 2.97 (s, 3H). MS (ESI) m/z 446 (M+H)⁺.

ii. Scheme 2: Synthesis of Compound 2

Compound 2:2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-146-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.85 (s, 1H), 8.48 (s, 1H), 8.18 (s, 1H),7.78-7.67 (m, 2H), 7.57-7.50 (m, 1H), 7.30-7.25 (m, 1H), 7.20 (td,J=7.6, 1.0 Hz, 1H), 6.71 (d, J=2.6 Hz, 1H), 6.61-6.53 (m, 1H), 3.86 (d,J=4.4 Hz, 1H), 3.83 (s, 2H), 3.54 (d, J=12.0 Hz, 2H), 3.29 (s, 2H),3.23-3.12 (m, 2H), 2.95 (t, J=12.5 Hz, 2H), 2.88 (s, 3H). MS (ESI) m/z528 (M+H)⁺

Compound 2 can be synthesized using the following Scheme 2.

In Scheme 2,2-chloro-11-methyl-5-(2,2,2-trifluoroethyl)-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(5) can be synthesized as follows: 1,2-chloro-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(3) (500 mg, 1.9 mmol), Cs₂CO₃ (1.3 g, 4.0 mmol) and trifluoroethyliodide (250 μL, 2.6 mmol) were dissolved in DMA (5 mL) and heated to 70°C. for 2 h. The solvent was evaporated and the residue purified bysilica column chromatography (0-5% MeOH in DCM) to give the titlecompound (116 mg, 18%). ¹H NMR (500 MHz, DMSO-d₆) δ 8.84 (s, 1H), 7.73(dd, J=7.8, 1.7 Hz, 1H), 7.59 (ddd, J=8.4, 7.3, 1.7 Hz, 1H), 7.34 (dd,J=8.4, 0.9 Hz, 1H), 7.26 (ddd, J=8.0, 7.3, 1.0 Hz, 1H), 5.04 (br s, 2H),3.38 (s, 3H). ¹³C NMR (126 MHz, DMSO-d₆) δ 167.79, 165.40, 155.37,149.08, 134.04, 132.42, 126.15, 125.90, 125.17, 124.92, 123.66, 119.15,48.61 (q, J=32.5 Hz), 36.30. MS (ESI) m/z 343 (M+H)⁺

Other steps in Scheme 2 can be performed as described in Scheme 1.

iii. Scheme 3: Synthesis of Compound 3

Compound 3:5-ethyl-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-055-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.75 (s, 1H), 8.35 (s, 1H), 7.81 (d, J=8.7Hz, 1H), 7.64 (dd, J=7.7, 1.7 Hz, 1H), 7.49 (ddd, J=8.7, 7.2, 1.7 Hz,1H), 7.24-7.13 (m, 2H), 6.72 (d, J=2.6 Hz, 1H), 6.57 (dd, J=8.8, 2.6 Hz,1H), 4.20-3.92 (m, 1H), 3.89 (s, 2H), 3.83 (s, 3H), 3.54 (d, J=12.1 Hz,2H), 3.28 (s, 3H), 3.18 (q, J=10.9 Hz, 2H), 2.94 (t, J=12.6 Hz, 2H),2.89 (d, J=3.4 Hz, 3H), 1.16 (t, J=7.1 Hz, 3H). MS (ESI) m/z 474 (M+H)⁺

Compound 3 can be synthesized using the following Scheme 3.

In Scheme 3,2-chloro-5-ethyl-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(6) can be synthesized as follows: 1,2-chloro-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(3) (500 mg, 1.9 mmol), Cs₂CO₃ (1.3 g, 4.0 mmol) and ethyl iodide (210μL, 2.6 mmol) were dissolved in DMA (5 mL) and heated to 70° C. for 2 h.The solvent was evaporated and the residue purified by silica columnchromatography (0-5% MeOH in DCM) to give the title compound (280 mg,51%). ¹H NMR (500 MHz, DMSO-d₆) δ 8.65 (s, 1H), 7.66 (dd, J=7.8, 1.7 Hz,1H), 7.53 (ddd, J=8.4, 7.3, 1.7 Hz, 1H), 7.27 (dd, J=8.4, 1.0 Hz, 1H),7.22 (td, J=7.5, 1.0 Hz, 1H), 4.10 (q, J=5.2 Hz, 2H), 3.18 (s, 3H), 1.20(t, J=7.1 Hz, 3H). ¹³C NMR (126 MHz, DMSO-d₆) δ 167.06, 164.74, 153.97,153.61, 148.71, 133.30, 132.08, 127.49, 126.71, 124.70, 118.82, 46.09,36.31, 13.82. MS (ESI) m/z 290 (M+H)⁺

Other steps in Scheme 3 can be performed as described in Scheme 1.

iv. Scheme 4: Synthesis of Compound 4

Compound 4 can be synthesized using the following Scheme 4.

In Scheme 4,2-chloro-5-isopropyl-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(7) can be synthesized as follows: 1,2-chloro-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(3) (500 mg, 1.9 mmol), Cs₂CO₃ (1.3 g, 4.0 mmol) and isopropyl iodide(250 μL, 2.2 mmol) were dissolved in DMA (5 mL) and heated to 70° C. for2 h. The solvent was evaporated and the residue purified by silicacolumn chromatography (0-5% MeOH in DCM) to give the title compound (167mg, 29%). ¹H NMR (500 MHz, DMSO-d₆) δ 8.58 (s, 1H), 7.69 (dd, J=7.8, 1.7Hz, 1H), 7.52 (ddd, J=8.3, 7.3, 1.7 Hz, 1H), 7.27 (dd, J=8.5, 1.1 Hz,1H), 7.21 (td, J=7.5, 1.0 Hz, 1H), 4.52 (hept, J=6.8 Hz, 1H), 3.35 (s,3H), 1.80-0.85 (m, 6H). ¹³C NMR (126 MHz, DMSO-d₆) δ 167.49, 166.18,154.39, 148.79, 133.11, 132.29, 126.90, 125.90, 124.56, 118.46, 54.22,36.01. MS (ESI) m/z 304 (M+H)⁺

Other steps in Scheme 4 can be performed as described in Scheme 1.

v. Other Compounds

All other compounds were prepared from intermediates (4), (5), (6) or(7) by analogous methods to XMD8-85 (Compound 1) as described herein.

Compound 5:5-ethyl-2-((4-(4-hydroxypiperidin-1-yl)-2-methoxyphenyl)amino)-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(XMD9-22)

¹H NMR (500 MHz, DMSO-d₆) δ 8.33 (s, 1H), 7.94 (s, 1H), 7.72 (d, J=8.8Hz, 1H), 7.63 (dd, J=7.7, 1.8 Hz, 1H), 7.50-7.45 (m, 1H), 7.21 (d, J=8.4Hz, 1H), 7.16 (t, J=7.4 Hz, 1H), 6.61 (d, J=2.6 Hz, 1H), 6.49 (dd,J=8.8, 2.6 Hz, 1H), 4.15-4.01 (m, 1H), 3.80 (s, 3H), 3.62 (tq, J=8.5,4.4 Hz, 1H), 3.55-3.46 (m, 2H), 3.35 (s, 2H), 3.27 (s, 3H), 1.83 (dq,J=12.4, 4.0 Hz, 2H), 1.50 (dtd, J=13.0, 9.5, 3.8 Hz, 2H), 1.15 (t, J=7.1Hz, 3H). MS (ESI) m/z 475 (M+H)⁺

Compound 6:5-isopropyl-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-149-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.71 (s, 1H), 8.25 (s, 1H), 8.11 (s, 1H),7.78 (d, J=8.7 Hz, 1H), 7.66 (dd, J=7.7, 1.7 Hz, 1H), 7.46 (ddd, J=8.7,7.2, 1.7 Hz, 1H), 7.27-7.12 (m, 2H), 6.71 (d, J=2.6 Hz, 1H), 6.57 (dd,J=8.8, 2.6 Hz, 1H), 4.60 (hept, J=6.8 Hz, 1H), 3.82 (s, 6H), 3.54 (d,J=12.2 Hz, 2H), 3.28 (s, 3H), 3.17 (dd, J=12.8, 9.2 Hz, 2H), 2.94 (t,J=12.7 Hz, 2H), 2.88 (d, J=3.3 Hz, 3H), 1.49-1.36 (m, 3H), 1.08 (d,J=6.8 Hz, 3H). MS (ESI) m/z 488 (M+H)⁺

Compound 7:4-((5-ethyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide(FMF-03-059-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.38 (s, 1H), 8.49 (s, 1H), 8.36 (dd, J=8.0,5.3 Hz, 2H), 8.23-8.16 (m, 1H), 7.66 (dd, J=7.8, 1.7 Hz, 1H), 7.60-7.54(m, 1H), 7.54-7.46 (m, 2H), 7.25 (dt, J=8.4, 1.9 Hz, 1H), 7.19 (td,J=7.5, 1.1 Hz, 1H), 4.61 (br s, 2H), 4.11-3.98 (m, 1H), 3.95 (d, J=3.8Hz, 3H), 3.49 (d, J=12.2 Hz, 2H), 3.36 (s, 3H), 3.17-3.05 (m, 2H), 2.79(d, J=4.6 Hz, 3H), 2.08-1.98 (m, 2H), 1.82-1.69 (m, 2H), 1.18 (t, J=7.0Hz, 3H). MS (ESI) m/z 516 (M+H)⁺

Compound 8:3-methoxy-4-((11-methyl-6-oxo-5-(2,2,2-trifluoroethyl)-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-N-(1-methylpiperidin-4-yl)benzamide(FMF-03-148-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.43 (s, 1H), 8.63 (s, 1H), 8.38 (d, J=7.5Hz, 1H), 8.34 (d, J=10.0 Hz, 1H), 8.29 (d, J=8.4 Hz, 1H), 7.71 (dd,J=7.7, 1.7 Hz, 1H), 7.56 (ddt, J=10.1, 8.7, 3.3 Hz, 2H), 7.53-7.48 (m,1H), 7.30 (dd, J=8.2, 3.0 Hz, 1H), 7.25-7.20 (m, 1H), 5.27 (s, 1H), 4.62(s, 1H), 4.17-3.97 (m, 1H), 3.94 (d, J=3.7 Hz, 3H), 3.48 (s, 2H), 3.37(d, J=2.8 Hz, 3H), 3.18-3.05 (m, 2H), 2.79 (d, J=4.6 Hz, 3H), 2.08-2.01(m, 2H), 1.78 (qd, J=13.7, 3.9 Hz, 2H).

MS (ESI) m/z 570 (M+H)⁺

Compound 9:4-((5-isopropyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide(FMF-03-151-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.44 (s, 1H), 8.39 (s, 1H), 8.33 (d, J=8.4Hz, 1H), 8.26 (s, 1H), 7.68 (dd, J=7.7, 1.8 Hz, 1H), 7.57 (dd, J=8.5,1.9 Hz, 1H), 7.52-7.46 (m, 2H), 7.24 (dt, J=8.7, 1.9 Hz, 1H), 7.18 (td,J=7.5, 1.0 Hz, 1H), 4.59 (p, J=6.8 Hz, 1H), 4.20-3.98 (m, 1H), 3.94 (d,J=3.9 Hz, 3H), 3.49 (d, J=12.2 Hz, 2H), 3.36 (s, 3H), 3.17-3.06 (m, 2H),2.79 (d, J=4.6 Hz, 3H), 2.09-1.99 (m, 2H), 1.78 (qd, J=13.6, 3.9 Hz,2H), 1.47 (s, 3H), 1.11 (s, 3H). MS (ESI) m/z 530 (M+H)⁺

Compound 10:N-(4-((5,11-dimethyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxyphenyl)methanesulfonamide(FMF-03-047-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.57 (s, 1H), 8.36 (s, 1H), 8.16 (s, 1H),7.98 (d, J=8.6 Hz, 1H), 7.69 (dd, J=7.8, 1.7 Hz, 1H), 7.51 (ddd, J=8.7,7.2, 1.8 Hz, 1H), 7.26 (d, J=8.3 Hz, 1H), 7.18 (t, J=7.5 Hz, 1H), 6.91(d, J=2.3 Hz, 1H), 6.84 (dd, J=8.6, 2.3 Hz, 1H), 3.82 (s, 3H), 3.39 (s,3H), 3.32 (s, 4H), 2.98 (s, 3H). MS (ESI) m/z 455 (M+H)⁺

Compound 11:N-(4-((5-ethyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxyphenyl)methanesulfonamide(FMF-03-087-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.57 (s, 1H), 8.39 (s, 1H), 8.16 (s, 1H),7.98 (d, J=8.6 Hz, 1H), 7.64 (dd, J=7.7, 1.7 Hz, 1H), 7.53-7.44 (m, 1H),7.24 (dd, J=8.4, 0.9 Hz, 1H), 7.17 (td, J=7.5, 1.0 Hz, 1H), 6.91 (d,J=2.4 Hz, 1H), 6.84 (dd, J=8.6, 2.3 Hz, 1H), 4.02 (s, 2H), 3.82 (s, 3H),3.31 (s, 3H), 2.98 (s, 3H), 1.16 (t, J=7.1 Hz, 3H). MS (ESI) m/z 469(M+H)⁺

Compound 12:N-(3-methoxy-4-((11-methyl-6-oxo-5-(2,2,2-trifluoroethyl)-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)phenyl)methanesulfonamide(FMF-03-147-1)

¹H NMR (500 MHz, DMSO-d₆) δ 8.65 (s, 1H), 7.72 (dd, J=7.8, 1.7 Hz, 1H),7.60-7.54 (m, 1H), 7.32 (dd, J=8.5, 1.0 Hz, 1H), 7.23 (td, J=7.5, 0.9Hz, 1H), 6.80 (s, 1H), 6.70 (d, J=1.3 Hz, 2H), 3.75 (s, 3H), 3.65 (s,2H), 3.29 (s, 3H), 3.17 (s, 3H). MS (ESI) m/z 523 (M+H)⁺

Compound 13:N-(4-((5-isopropyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxyphenyl)methanesulfonamide(FMF-03-150-2)

¹H NMR (500 MHz, DMSO-d₆) δ 9.57 (s, 1H), 8.30 (s, 1H), 8.16 (s, 1H),7.96 (d, J=8.6 Hz, 1H), 7.66 (dd, J=7.8, 1.7 Hz, 1H), 7.50-7.43 (m, 1H),7.25-7.21 (m, 2H), 7.16 (td, J=7.5, 1.0 Hz, 1H), 6.91 (d, J=2.3 Hz, 1H),6.83 (dd, J=8.6, 2.3 Hz, 1H), 4.55 (dq, J=38.7, 6.8 Hz, 1H), 3.81 (s,3H), 3.30 (s, 3H), 2.98 (s, 3H), 1.44 (d, J=5.6 Hz, 4H), 1.09 (d, J=6.6Hz, 4H).

MS (ESI) m/z 483 (M+H)⁺

Compound 14:5-ethyl-2-((2-methoxy-4-(4-(pyrrolidin-1-yl)piperidine-1-carbonyl)phenyl)amino)-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-058-2)

¹H NMR (500 MHz, DMSO-d₆) δ 9.78 (s, 1H), 8.47 (s, 1H), 8.29 (d, J=8.2Hz, 1H), 8.20 (s, 1H), 7.66 (dd, J=7.7, 1.7 Hz, 1H), 7.50 (ddd, J=8.7,7.3, 1.8 Hz, 1H), 7.25 (dd, J=8.4, 1.0 Hz, 1H), 7.19 (td, J=7.5, 1.0 Hz,1H), 7.09-7.00 (m, 2H), 4.05 (s, 2H), 3.91 (s, 3H), 3.53 (s, 2H),3.47-3.37 (m, 1H), 3.35 (s, 3H), 3.16-3.05 (m, 2H), 2.96 (s, 1H), 2.55(s, 2H), 2.09 (s, 2H), 2.06-1.92 (m, 2H), 1.93-1.78 (m, 2H), 1.63-1.49(m, 1H), 1.17 (t, J=7.1 Hz, 3H).

MS (ESI) m/z 556 (M+H)⁺

Compound 15:N-(4-((5-ethyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)phenyl)methanesulfonamide(FMF-03-083-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.66 (s, 1H), 9.44 (s, 1H), 8.43 (s, 1H),7.74-7.68 (m, 2H), 7.64 (dd, J=7.7, 1.7 Hz, 1H), 7.48 (ddd, J=8.8, 7.2,1.7 Hz, 1H), 7.26 (dd, J=8.4, 1.0 Hz, 1H), 7.16 (d, J=8.8 Hz, 3H),4.15-3.59 (m, 2H), 3.35 (s, 3H), 2.93 (s, 3H), 1.17 (t, J=7.0 Hz, 3H).

MS (ESI) m/z 439 (M+H)⁺

Compound 16:5-ethyl-2-((2-methoxy-4-(2-(4-methylpiperazin-1-yl)ethoxy)phenyl)amino)-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-086-1)

¹H NMR (500 MHz, DMSO-d₆) δ 8.35 (s, 1H), 8.14 (s, 1H), 7.79 (d, J=8.7Hz, 1H), 7.64 (dd, J=7.7, 1.7 Hz, 1H), 7.48 (ddd, J=8.7, 7.2, 1.8 Hz,1H), 7.25-7.12 (m, 2H), 6.66 (d, J=2.7 Hz, 1H), 6.58 (dd, J=8.8, 2.7 Hz,1H), 4.21 (t, J=5.2 Hz, 2H), 4.05 (s, 2H), 3.81 (s, 3H), 3.41 (s, 4H),3.27 (s, 3H), 3.17 (s, 4H), 2.82 (s, 3H), 1.16 (t, J=7.1 Hz, 3H).

MS (ESI) m/z 518 (M+H)⁺

Compound 17:4-((5-ethyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)benzenesulfonamide(FMF-03-088-1/-2)

¹H NMR (500 MHz, DMSO-d₆) δ 10.07 (s, 1H), 8.51 (s, 1H), 7.95-7.88 (m,2H), 7.79-7.72 (m, 2H), 7.66 (dd, J=7.8, 1.7 Hz, 1H), 7.53-7.47 (m, 1H),7.27 (dd, J=8.4, 1.0 Hz, 1H), 7.21-7.15 (m, 3H), 3.53 (s, 2H), 3.39 (s,3H), 1.18 (t, J=7.1 Hz, 3H). MS (ESI) m/z 425 (M+H)⁺

Compound 18:N-(2-(dimethylamino)ethyl)-4-((5-ethyl-11-methyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)-3-methoxybenzamide(FMF-03-061-1)

¹H NMR (500 MHz, DMSO-d₆) δ 9.41 (s, 1H), 8.64 (t, J=5.7 Hz, 1H), 8.50(s, 1H), 8.38 (d, J=8.5 Hz, 1H), 8.23 (s, 1H), 7.66 (dd, J=7.7, 1.7 Hz,1H), 7.57 (dd, J=8.5, 1.9 Hz, 1H), 7.53 (d, J=2.0 Hz, 1H), 7.50 (ddd,J=8.8, 7.2, 1.7 Hz, 1H), 7.25 (dd, J=8.4, 1.0 Hz, 1H), 7.19 (td, J=7.5,1.0 Hz, 1H), 4.09 (s, 2H), 3.94 (s, 3H), 3.62 (q, J=5.9 Hz, 2H), 3.36(s, 3H), 3.28 (q, J=5.9 Hz, 2H), 2.87 (d, J=4.7 Hz, 6H), 1.18 (t, J=7.0Hz, 3H). MS (ESI) m/z 490 (M+H)⁺

Compound 19:2-((4-(3-(dimethylamino)pyrrolidine-1-carbonyl)-2-methoxyphenyl)amino)-5-ethyl-11-methyl-5,11-dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one(FMF-03-067-1)

¹H NMR (500 MHz, DMSO-d₆) δ 10.17 (s, 1H), 8.48 (s, 1H), 8.32 (d, J=8.2Hz, 1H), 8.22 (s, 1H), 7.66 (dd, J=7.7, 1.7 Hz, 1H), 7.50 (ddd, J=8.7,7.3, 1.7 Hz, 1H), 7.27-7.15 (m, 4H), 3.95 (s, 2H), 3.92 (s, 3H),3.75-3.66 (m, 2H), 3.61 (s, 2H), 3.35 (s, 3H), 2.85 (s, 6H), 2.40-2.26(m, 1H), 2.12 (t, J=10.6 Hz, 1H), 1.17 (t, J=7.0 Hz, 3H).

MS (ESI) m/z 516 (M+H)⁺

Selectivity Data

FIG. 1 illustrates the selectivity of Compound 2 (FMF-03-146-1) at aconcentration of 1 μM against a panel of 468 human kinases and humanmutant kinases. These selectivity data were generated using KINOMEscan®platform and these images were generated using TREEspot™ Software Tooland reprinted with permission from KINOMEscan®, a division of DiscoveRxCorporation, © DISCOVERX CORPORATION 2010.

Biochemical Assay General Material Lysis Buffer

50 mM HEPES pH 7.8

350 mM NaCl

20 mM imidazole

5% Glycerol

Wash Buffer 1—Same as Lysis

Wash Buffer 2 and 3—Same as lysis but 25 mM ImidazoleElution Buffer—Same as lysis but 300 mM ImidazoleS200 Gel filtration Buffer

10 mM HEPES pH 7.8

700 mM NaCl

1 mM MgCl2

5% Glycerol

Substrate for Gel Shift Assay

5-FAM-KKLRRTLSVA-COOH

DCLK1 Plasmid Construct

The DNA construct consisting of N-terminally 6-His tagged human DCLK1residues G351-H689 was prepared. Thus prepared plasmid wasco-transformed with lambda phosphatase under chloramphenicol selectioninto BL21(DE3) E. coli cells.

DCLK1 Protein Purification

Protein expression was induced from the DCLK1 plasmid with 0.6 mM IPTGand expression was allowed to continue for about 10 hours at atemperature of 18° C. Cells was harvested by centrifugation andresuspended in Lysis buffer with protease inhibitors (1 mM Benzamidineand 1 mM PMSF). Lysis was performed by passing 3 times through ahomogenizer. Lysate was centrifuged at 20K for 1 hour at a temperatureof 4° C. and the supernatant was filtered through a 0.2 micron membrane.Protein was loaded on nickel (Ni)-NTA resin, washed with Wash buffers,and eluted with 300 mM imidazole buffer. Eluate was concentrated to 2 mLand passed over a Superdex 5200 column.

DCLK1 Mobility Shift Assay (Gel Shift Assay)

DCLK1 kinase activity was measured in vitro using an electrophoreticmobility shift assay. The reaction was assembled in a 384-well plate ina total volume of 20 μl. The reaction contained 30 nM recombinant DCLK1,one DCLK1 inhibitor or DMSO, 100 μM ATP and 1 μM FAM-labeled peptidesubstrate in a buffer (100 mM HEPES pH 7.5, 0.003% Brij-35, 0.004%Tween-20, 10 mM MgCl₂, and 2 mM DTT). DCLK1 inhibitors were dispensedusing a Labcyte Echo liquid handler. The reaction was incubated at roomtemperature for two hours and quenched by addition of 40 μL oftermination buffer (100 mM HEPES pH 7.3, 0.015% Brij-35, 0.1% CR-3,1×CR-8, and 40 mM EDTA). Substrate and product peptides present in eachsample were electrophoretically separated and detected using 12-channelLabChip3000 microfluidic capillary electrophoresis instrument (CaliperLife Sciences, Waltham Mass., USA). The change in the relativefluorescence intensities of substrate and product peaks (reflectingenzyme activity) was measured. Capillary electrophoregrams were analyzedusing HTS Well Analyzer software (Caliper Life Sciences, Waltham Mass.,USA).

The kinase activity in each sample was determined as the product-to-sumratio (PSR):P/(S+P), where P is the peak height of the product peptideand S is the peak height of the substrate peptide. Negative controlsamples (DMSO in the absence of inhibitor) and positive control samples(100% inhibition, a tested DCLK1 inhibitor) were assembled in replicatesand were used to calculate percent inhibition values for each compoundat each concentration.

Percent inhibition (% Inhibition) was determined using the followingequation:

${{\% \mspace{14mu} {Inhibition}} = {100 \times \frac{\left( {{PSR}_{0\%} - {PSR}_{inh}} \right)}{\left( {{PSR}_{0\%} - {PSR}_{100\%}} \right)}}},$

where PSR_(inh) is the product-sum ratio in the presence of inhibitor,PSR_(0%) is the average product-sum ration in the absence of inhibitorand PSR_(100%) is the average product-sum ratio in 100%-inhibitioncontrol samples.

The DCLK1 candidate inhibitors were tested in 8-point dose-responseformat on each assay plate. The IC₅₀ values were determined by fittingthe inhibition curves by an eight dose-response model using GraphPadPrism 7 software.

FIG. 2 shows the thus obtained IC₅₀ values of Compound 7, Compound 15,Compound 11, Compound 8, Compound 16 and Compound 12. In particular, theIC₅₀ values of Compound 7 and Compound 11 were substantatially decreasedfrom the IC₅₀ value of the positive control.

INCORPORATION BY REFERENCE

The contents of all references (including literature references, issuedpatents, published patent applications, and co-pending patentapplications) cited throughout this application are hereby expresslyincorporated herein in their entireties by reference. Unless otherwisedefined, all technical and scientific terms used herein are accorded themeaning commonly known to one with ordinary skill in the art.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents of the specificembodiments of the invention described herein. Such equivalents areintended with be encompassed by the following claims.

REFERENCES

-   1. Reiner, O.; Coquelle, F. M.; Peter, B.; Levy, T.; Kaplan, A.;    Sapir, T.; Orr, I.; Barkai, N.; Eichele, G.; Bergmann, S., The    evolving doublecortin (DCX) superfamily. BMC Genomics 2006, 7 (1),    1-16.-   2. The Cancer Genome Atlas Research, N., Comprehensive molecular    characterization of gastric adenocarcinoma. Nature 2014, 513 (7517),    202-209.-   3. Győrffy, B.; Surowiak, P.; Budczies, J.; Lánczky, A., Online    Survival Analysis Software to Assess the Prognostic Value of    Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer.    PLoS ONE 2013, 8 (12), e82241.-   4. (a) Ito, H.; Tanaka, S.; Akiyama, Y.; Shimada, S.; Adikrisna, R.;    Matsumura, S. Aihara, A.; Mitsunori, Y.; Ban, D.; Ochiai, T.; Kudo,    A.; Arii, S.; Yamaoka, S.; Tanabe, M., Dominant Expression of DCLK1    in Human Pancreatic Cancer Stem Cells Accelerates Tumor Invasion and    Metastasis. PLoS ONE 2016, 11 (1), e0146564; (b) Nakanishi, Y.;    Seno, H.; Fukuoka, A.; Ueo, T.; Yamaga, Y.; Maruno, T. Nakanishi,    N.; Kanda, K.; Komekado, H.; Kawada, M.; Isomura, A.; Kawada, K.;    Sakai, Y.; Yanagita, M.; Kageyama, R.; Kawaguchi, Y.; Taketo, M. M.;    Yonehara, S.; Chiba, T., Dclk1 distinguishes between tumor and    normal stem cells in the intestine. Nature genetics 2013, 45 (1),    98-103; (c) Westphalen, C. B.; Asfaha, S.; Hayakawa, Y.; Takemoto,    Y.; Lukin, D. J.; Nuber, A. H.; Brandtner, A.; Setlik, W.; Remotti,    H.; Muley, A.; Chen, X.; May, R.; Houchen, C. W.; Fox, J. G.;    Gershon, M. D.; Quante, M.; Wang, T. C., Long-lived intestinal tuft    cells serve as colon cancer-initiating cells. The Journal of    clinical investigation 2014, 124 (3), 1283-95; (d) Westphalen, C.    B.; Takemoto, Y.; Tanaka, T.; Macchini, M.; Jiang, Z.; Renz, B. W.;    Chen, X.; Ormanns, S.; Nagar, K.; Tailor, Y.; May, R.; Cho, Y.;    Asfaha, S.; Worthley, D. L.; Hayakawa, Y.; Urbanska, A. M.; Quante,    M.; Reichert, M.; Broyde, J.; Subramaniam, P. S.; Remotti, H.;    Su, G. H.; Rustgi, A. K.; Friedman, R. A.; Honig, B.; alifano, A.;    Houchen, C. W.; Olive, K. P.; Wang, T. C., Dclk1 Defines Quiescent    Pancreatic Progenitors that Promote Injury-Induced Regeneration and    Tumorigenesis. Cell Stem Cell 18 (4), 441-455.

1. A method of treating a disease in a subject wherein the disease ismediated by doublecortin-like kinase (DCLK1) and/or DCLK2, or a methodfor reducing DCLK1/2-dependent cell growth, or a method of inhibitingDCLK1/2 in a subject identified as in need of such treatment, the methodcomprising administering to the subject a compound of formula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic,wherein R₁ may be optionally substituted; R₂ is hydrogen or optionallysubstituted alkyl; R₅ is hydrogen or methyl, optionally substitutedalkyl, optionally substituted aralkyl, or optionally substitutedcarbocyclic; and R₆ is hydrogen or optionally substituted alkyl; each R₇is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and p is 0-4.
 2. (canceled)
 3. The method of claim 1,wherein R₂ is (i) unsubstituted alkyl; or (ii) methyl, ethyl, propyl, oriso-propyl, each of which may be optionally substituted with one or morehalogens; or (iii) —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃. 4.-5. (canceled)6. The method of claim 1, wherein the compound is of formula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof.
 7. Themethod of claim 1, wherein R₁ is (i) methyl, ethyl, propyl, iso-propyl,butyl, s-butyl, t-butyl, pentyl, hexyl, cyclohexyl, piperidinyl,pyrrolidino, phenyl, 1-naphthyl, 2-naphthyl, pyridyl, pyrimidinyl,pyrazinyl, pyridizinyl, quinolinyl, thienyl, thiazolyl, oxazolyl,isoxazolyl, pyrrolyl, furanyl, isoquinolinyl, imiazolyl, or triazolyl,each of which may be optionally substituted; or (ii) phenyl or pyridyl,each of which may be optionally substituted; or (iii) substituted with0-4 substituents, selected from halo, nitro, cyano, hydroxyl, amino,NH(R_(A)), N(R_(A))(R_(A)), CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂,C(O)NH(R_(A)), C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy,heteroaryl, heterocyclic, and carbocyclic, each of which may be furthersubstituted; wherein each R_(A) is independently selected from alkyl,alkenyl, carbocyclic, aryl, heteroaryl, and heterocyclic, or two R_(A)on the same atom combine to form a heterocyclic, each of which may befurther substituted; or (iv) substituted with 0-4 substituents, selectedfrom alkoxy, CO₂Me,

or (v) phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl, pyrazolyl,imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each of which may beoptionally substituted; or (vi) substituted with 0-4 substituents,selected from halo, nitro, cyano, hydroxyl, amino, NH(R_(A)),N(R_(A))(R_(A)), CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, carbocyclic, SO₂(R_(A)), SO₃(R_(A)), SO₂N(R_(A))(R_(A)),SO₂NH(R_(A)), SO₂NH₂, PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each ofwhich may be further substituted; and wherein each R_(A) isindependently selected from alkyl, alkenyl, carbocyclic, aryl,heteroaryl, and heterocyclic, or two R_(A) on the same atom combine toform a heterocyclic, each of which may be further substituted; or (vii)selected from the group consisting of:

8.-13. (canceled)
 14. The method of claim 1, wherein the compoundinhibits DCLK1 and/or DCLK2.
 15. The method of claim 1, wherein thedisease is: (i) cancer or a proliferation disease selected from thegroup consisting of Barretts' esophagus, esophageal cancer, salivarygland malignancies, colon and colorectal cancer, intestinal cancer,gastric cancer, pancreatic cancer, skin cancer and neuroblastoma; or(ii) a liver disease such as a fatty liver disease selected from thegroup consisting of non-alcoholic fatty acid liver disease (NAFLD),non-alcoholic steatohepatitis (NASH), fatty liver disease resulting fromhepatitis, fatty liver disease resulting from obesity, fatty liverdisease resulting from diabetes, fatty liver disease resulting frominsulin resistance, fatty liver disease resulting fromhypertriglyceridemia, Abetalipoproteinemia, glycogen storage diseases,Weber-Christian disease, Wolmans disease, acute fatty liver ofpregnancy, and lipodystrophy. 16.-18. (canceled)
 19. The method of claim1, wherein the subject is administered simultaneously or sequentially anadditional therapeutic agent, wherein the additional therapeutic agentcomprises an anti-inflammatory agent or a chemotherapeutic agent.20.-23. (canceled)
 24. The method of claim 1, wherein the subject is ahuman.
 25. The method of claim 1, wherein the compound has a Ki forinhibiting the DCLK1/2 less than about 15 nM. 26.-37. (canceled)
 38. Amethod of treating a disease in a subject wherein the disease ismediated by a kinase that is doublecortin-like kinase (DCLK1/2), or amethod for reducing DCLK1/2-dependent cell growth, or a method ofinhibiting DCLK1/2 in a subject identified as in need of such treatment,the method comprising administering to the subject a compound of formulaA-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, X is CHR₄, CR₄, NH, NR₄ or N; Y is NR₅, N, S, SO, SO₂, O, CHR₅,or CR₅; wherein at least one of X and Y is NH, NR₄, NR₅, N, S, SO, SO₂,or O; A is a single bond or double bond; B is a single bond or doublebond, wherein both A and B are not double bonds; R′ is H or alkyl; L isabsent, S, SO, SO₂, or CO; R₁ is H, alkyl, alkenyl, alkynyl, eachcontaining 0, 1, 2, or 3 heteroatoms selected from O, S, or N; or R₁ isaryl, arylalkyl, heteroaryl, heterocyclic, or carbocyclic; wherein R₁may be optionally substituted; R₂ is hydrogen or optionally substitutedalkyl; R₃ is hydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic, each of which may be optionallysubstituted; R₄ is hydrogen, alkyl, alkenyl, aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic, each of which may beoptionally substituted; R₅ is hydrogen, alkyl, alkenyl, aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic, each of which may beoptionally substituted; or R₃ and X, together with the atoms to whichthey are attached, form a 3-8 membered carbocyclic, aryl, heterocyclic,or heteroaryl; each of which is optionally substituted; or X and Y,together with the atoms to which they are attached, form a 3-8 memberedcarbocyclic, aryl, heterocyclic, or heteroaryl; each of which isoptionally substituted; and R₆ is hydrogen or optionally substitutedalkyl. 39.-40. (canceled)
 41. The method of claim 38, wherein thecompound has a structure according to formula B-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is aryl, or heteroaryl, wherein R₁ may be optionallysubstituted; R₂ is hydrogen or optionally substituted alkyl; R₃ ishydrogen or methyl; R₄ is hydrogen or methyl; and R₆ is hydrogen; orwherein the compound has a structure according to formula C-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is aryl, heteroaryl, which may be optionally substituted; R₂is hydrogen or methyl; R₃ is hydrogen; R₄ is hydrogen; and R₆ ishydrogen; or wherein the compound has a structure according to formulaD-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic,wherein R₁ may be optionally substituted; R₂ is hydrogen or optionallysubstituted alkyl; R₆ is hydrogen or optionally substituted alkyl; eachR₇ is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and p is 0-6; or wherein the compound has a structureaccording to formula E-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic,wherein R₁ may be optionally substituted; R₂ is hydrogen or optionallysubstituted alkyl; R₃ is hydrogen or optionally substituted alkyl; R₆ ishydrogen or optionally substituted alkyl; each R₇ is independentlyalkyl, alkenyl, aryl, arylalkyl, heteroaryl, heterocyclic, carbocyclic,alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl), or N(alkyl)(aryl), each ofwhich may be optionally substituted; halo, nitro, or cyano; and p is0-6; or wherein the compound has a structure according to formula F-I:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, Y is S, SO, SO₂, or O; R₁ is alkyl, aryl, heteroaryl,heterocyclic, or carbocyclic, wherein R₁ may be optionally substituted;R₂ is hydrogen or optionally substituted alkyl; R₆ is hydrogen oroptionally substituted alkyl; each R₇ is independently alkyl, alkenyl,aryl, arylalkyl, heteroaryl, heterocyclic, carbocyclic, alkoxy,NH(alkyl), NH(aryl), N(alkyl)(alkyl), or N(alkyl)(aryl), each of whichmay be optionally substituted; halo, nitro, or cyano; and p is 0-4; orwherein the compound has a structure according to formula G-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic, wherein R₁ may be optionallysubstituted; R₂ is hydrogen or optionally substituted alkyl; R₃ ishydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic, each of which may be optionally substituted; R₅ ishydrogen, alkyl, alkenyl, aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic, each of which may be optionally substituted; and R₆ ishydrogen or optionally substituted alkyl. 42.-46. (canceled)
 47. Amethod of treating a disease in a subject wherein the disease ismediated by doublecortin-like kinase (DCLK1) and/or doublecortin-likekinase 2 (DCLK2), or a method of inhibiting DCLK1/2 in a subjectidentified as in need of such treatment, or a method of reducingDCLK1/2-dependent cell growth, the method comprising administering tothe subject a compound selected from the group consisting of: formulaI-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, A is a single bond or double bond; R′ is H or alkyl; L isabsent, S, SO, SO₂, or CO; X is an optional substituent; R₁ is H, alkyl,alkenyl, alkynyl, each containing 0, 1, 2, or 3 heteroatoms selectedfrom O, S, or N; or R₁ is aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic; wherein R₁ may be optionally substituted; R₂ is hydrogen,optionally substituted alkyl, optionally substituted cycloalkyl, andoptionally substituted heterocyclyl; and R₆ is hydrogen or optionallysubstituted alkyl, formula II-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; E is NR₂ or CHR₂; R₁ isH, alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3 heteroatomsselected from O, S, or N; or R₁ is aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic; wherein R₁ may be optionally substituted;R₂ is, independently for each occurrence, hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; and R₆ is hydrogen or optionally substitutedalkyl, formula III-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; R₁ is H, alkyl, alkenyl,alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S,or N; or R₁ is aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic; wherein R₁ may be optionally substituted; R₂ is,independently for each occurrence, hydrogen, optionally substitutedalkyl, optionally substituted cycloalkyl, and optionally substitutedheterocyclyl; and R₆ is hydrogen or optionally substituted alkyl,formula IV-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; R₁ is H, alkyl, alkenyl,alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S,or N; or R₁ is aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic; wherein R₁ may be optionally substituted; R₂ is,independently for each occurrence, hydrogen, optionally substitutedalkyl, optionally substituted cycloalkyl, and optionally substitutedheterocyclyl; and R₆ is hydrogen or optionally substituted alkyl,formula V-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, X is an optional substituent as defined for formula I; R₂ ishydrogen or optionally substituted alkyl; R₃ is —OH or —O-(optionallysubstituted alkyl); R₄ is hydrogen or optionally substituted alkyl; andR₆ is hydrogen or optionally substituted alkyl, or formula VI-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; R₁ is H, alkyl, alkenyl,alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S,or N; or R₁ is aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic; wherein R₁ may be optionally substituted; R₂ is,independently for each occurrence, hydrogen, optionally substitutedalkyl, optionally substituted cycloalkyl, and optionally substitutedheterocyclyl; or two X moieties on adjacent atoms of the thiophene ringcan form, together with the atoms to which they are attached, a phenylring; and R₆ is hydrogen or optionally substituted alkyl, formula VII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; R₁ is H, alkyl, alkenyl,alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S,or N; or R₁ is aryl, arylalkyl, heteroaryl, heterocyclic, orcarbocyclic; wherein R₁ may be optionally substituted; R₂ is hydrogen,optionally substituted alkyl, optionally substituted cycloalkyl, andoptionally substituted heterocyclyl; and R₆ is hydrogen or optionallysubstituted alkyl, formula VIII-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R′ is H or alkyl; L is absent, S, SO, SO₂, or CO; X is anoptional substituent as defined for formula I; Z is O or S; R₁ is H,alkyl, alkenyl, alkynyl, each containing 0, 1, 2, or 3 heteroatomsselected from O, S, or N; or R₁ is aryl, arylalkyl, heteroaryl,heterocyclic, or carbocyclic; wherein R₁ may be optionally substituted;R₂ is hydrogen, optionally substituted alkyl, optionally substitutedcycloalkyl, and optionally substituted heterocyclyl; and R₆ is hydrogenor optionally substituted alkyl, and formula IX-2:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, A is a single bond or double bond; R′ is H or alkyl; L isabsent, S, SO, SO₂, or CO; Y is hydrogen, optionally substituted alkyl,optionally substituted cycloalkyl, and optionally substitutedheterocyclyl; R₁ is H, alkyl, alkenyl, alkynyl, each containing 0, 1, 2,or 3 heteroatoms selected from O, S, or N; or R₁ is aryl, arylalkyl,heteroaryl, heterocyclic, or carbocyclic; wherein R₁ may be optionallysubstituted; R₂ and R₂′ are each independently hydrogen, optionallysubstituted alkyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclyl; or Y and R₂′ can form, together with the atomsto which they are attached, a five-membered ring; and R₆ is hydrogen oroptionally substituted alkyl. 48.-73. (canceled)
 74. A compound offormula F-1:

or a pharmaceutically acceptable salt, ester or prodrug thereof,wherein, R₁ is alkyl, aryl, heteroaryl, heterocyclic, or carbocyclic,wherein R₁ may be optionally substituted; R₂ is hydrogen or optionallysubstituted alkyl; R₅ is hydrogen or methyl, optionally substitutedalkyl, optionally substituted aralkyl, or optionally substitutedcarbocyclic; and R₆ is hydrogen or optionally substituted alkyl; each R₇is independently alkyl, alkenyl, aryl, arylalkyl, heteroaryl,heterocyclic, carbocyclic, alkoxy, NH(alkyl), NH(aryl), N(alkyl)(alkyl),or N(alkyl)(aryl), each of which may be optionally substituted; halo,nitro, or cyano; and p is 0-4.
 75. (canceled)
 76. The compound of claim74, wherein R₂ is (i) unsubstituted alkyl; or (ii) methyl, ethyl,propyl, or iso-propyl, each of which may be optionally substituted withone or more halogen; or (iii) —CH₂—CH₂F, —CH₂—CHF₂, or —CH₂—CF₃. 77.-78.(canceled)
 79. The compound of claim 74, wherein the compound is offormula F-1-a:

or a pharmaceutically acceptable salt, ester or prodrug thereof.
 80. Thecompound of claim 74, wherein R₁ is (i) methyl, ethyl, propyl,iso-propyl, butyl, s-butyl, t-butyl, pentyl, hexyl, cyclohexyl,piperidinyl, pyrrolidino, phenyl, 1-naphthyl, 2-naphthyl, pyridyl,pyrimidinyl, pyrazinyl, pyridizinyl, quinolinyl, thienyl, thiazolyl,oxazolyl, isoxazolyl, pyrrolyl, furanyl, isoquinolinyl, imiazolyl, ortriazolyl, each of which may be optionally substituted; or (ii) phenylor pyridyl, each of which may be optionally substituted; or (iii)substituted with 0-4 substituents, selected from halo, nitro, cyano,hydroxyl, amino, NH(R_(A)), N(R_(A))(R_(A)), CO₂H, C(O)R_(A),C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)), C(O)N(R_(A))(R_(A)), alkyl, aryl,arylalkyl, alkoxy, heteroaryl, heterocyclic, and carbocyclic, each ofwhich may be further substituted; wherein each R_(A) is independentlyselected from alkyl, alkenyl, carbocyclic, aryl, heteroaryl, andheterocyclic, or two R_(A) on the same atom combine to form aheterocyclic, each of which may be further substituted; or (iv)substituted with 0-4 substituents, selected from alkoxy, CO₂Me,

or (v) phenyl, pyridyl, pyrimidinyl, furyl, pyrrolyl, pyrazolyl,imidazolyl, thienyl, or bicyclo[1.1.1]pent-1-yl, each of which may beoptionally substituted; or (vi) substituted with 0-4 substituents,selected from halo, nitro, cyano, hydroxyl, amino, NH(R_(A)),N(R_(A))(R_(A)), CO₂H, C(O)R_(A), C(O)OR_(A), C(O)NH₂, C(O)NH(R_(A)),C(O)N(R_(A))(R_(A)), alkyl, aryl, arylalkyl, alkoxy, heteroaryl,heterocyclic, carbocyclic, SO₂(R_(A)), SO₃(R_(A)), SO₂N(R_(A))(R_(A))SO₂NH(R_(A)), SO₂NH₂, PO(OR_(A))(OR_(A)), or PO(OR_(A))(R_(A)), each ofwhich may be further substituted; and wherein each R_(A) isindependently selected from alkyl, alkenyl, carbocyclic, aryl,heteroaryl, and heterocyclic, or two R_(A) on the same atom combine toform a heterocyclic, each of which may be further substituted; or (vii)selected from the group consisting of:

81.-86. (canceled)
 87. The compound of claim 74, wherein the compoundinhibits DCLK1 and/or DCLK2.
 88. A pharmaceutical composition comprisingthe compound of claim 74, or a pharmaceutically acceptable salt, esteror prodrug thereof. 89.-91. (canceled)